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BMRB: 25065

2MR8

holo structure of the Peptidyl Carrier Protein Domain 7 of the teicoplanin producing Non-ribosomal peptide synthetase

Authors

Haslinger, K., Maximowitsch, E., Redfield, C., Cryle, M.J.

Assembly

PCP7T holo form

Entity

1. PCP7T (polymer, Thiol state: all free), 91 monomers, 9618.939 Da Detail

GAMAKAPESA TEKVLCALYA EILGVERVGV DDAFHDLGGS SALAMRLIAR IREELGVDLP IRQLFSSPTP AGVARALAAK SASWSHPQFE K

2. 4'-PHOSPHOPANTETHEINE (non-polymer), 358.348 Da

Total weight

9977.287 Da

Max. entity weight

9618.939 Da

Entity Connection

metal coordination 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:SER41:SG	2:PNS1:O25

Source organism

Actinoplanes teichomyceticus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 96.7 %, Completeness: 71.5 %, Completeness (bb): 65.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.5 % (716 of 1001)	85.2 % (439 of 515)	62.7 % (249 of 397)	31.5 % (28 of 89)
Backbone	65.9 % (353 of 536)	88.6 % (163 of 184)	60.9 % (162 of 266)	32.6 % (28 of 86)
Sidechain	79.4 % (436 of 549)	83.4 % (276 of 331)	74.4 % (160 of 215)	0.0 % (0 of 3)
Aromatic	17.2 % (10 of 58)	34.5 % (10 of 29)	0.0 % (0 of 28)	0.0 % (0 of 1)
Methyl	95.7 % (111 of 116)	96.6 % (56 of 58)	94.8 % (55 of 58)

1. PCP7T

GAMAKAPESA TEKVLCALYA EILGVERVGV DDAFHDLGGS SALAMRLIAR IREELGVDLP IRQLFSSPTP AGVARALAAK SASWSHPQFE K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
5	PCP7T	natural abundance	500 uM
6	TRIS	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
13	PCP7T	natural abundance	500 uM
14	TRIS	natural abundance	50 mM
15	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 90.1 %, Completeness: 62.9 %, Completeness (bb): 59.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.9 % (1260 of 2002)	81.0 % (834 of 1030)	40.7 % (323 of 794)	57.9 % (103 of 178)
Backbone	59.2 % (635 of 1072)	86.4 % (318 of 368)	40.8 % (217 of 532)	58.1 % (100 of 172)
Sidechain	64.7 % (710 of 1098)	76.9 % (509 of 662)	46.0 % (198 of 430)	50.0 % (3 of 6)
Aromatic	21.6 % (25 of 116)	41.4 % (24 of 58)	0.0 % (0 of 56)	50.0 % (1 of 2)
Methyl	76.3 % (177 of 232)	92.2 % (107 of 116)	60.3 % (70 of 116)

1. PCP7T

GAMAKAPESA TEKVLCALYA EILGVERVGV DDAFHDLGGS SALAMRLIAR IREELGVDLP IRQLFSSPTP AGVARALAAK SASWSHPQFE K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
5	PCP7T	natural abundance	500 uM
6	TRIS	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
13	PCP7T	natural abundance	500 uM
14	TRIS	natural abundance	50 mM
15	D2O	natural abundance	100 %

Chem. Shift Complete3

Sequence coverage: 98.9 %, Completeness: 62.1 %, Completeness (bb): 56.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.1 % (1864 of 3003)	85.2 % (1317 of 1545)	35.2 % (419 of 1191)	47.9 % (128 of 267)
Backbone	56.4 % (907 of 1608)	88.9 % (491 of 552)	36.5 % (291 of 798)	48.4 % (125 of 258)
Sidechain	64.7 % (1066 of 1647)	82.5 % (819 of 993)	37.8 % (244 of 645)	33.3 % (3 of 9)
Aromatic	31.6 % (55 of 174)	56.3 % (49 of 87)	6.0 % (5 of 84)	33.3 % (1 of 3)
Methyl	71.6 % (249 of 348)	94.8 % (165 of 174)	48.3 % (84 of 174)

1. PCP7T

GAMAKAPESA TEKVLCALYA EILGVERVGV DDAFHDLGGS SALAMRLIAR IREELGVDLP IRQLFSSPTP AGVARALAAK SASWSHPQFE K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
5	PCP7T	natural abundance	500 uM
6	TRIS	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
13	PCP7T	natural abundance	500 uM
14	TRIS	natural abundance	50 mM
15	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MR8, Strand ID: A Detail

Release date

2015-01-25

Citation

Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis
Haslinger, K., Maximowitsch, E., Brieke, C., Koch, A., Redfield, C., Cryle, M.J.
Proteins (2015), 83, 711-721, PubMed 25586301 , DOI 10.1002/prot.24758 , Abstract

Related entities 1. PCP7T, : 1 : 1 : 123 entities Detail

Experiments performed 17 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

2 2D 1H-1H NOESY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
13	PCP7T	natural abundance	500 uM
14	TRIS	natural abundance	50 mM
15	D2O	natural abundance	100 %

3 3D 1H-13C NOESY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

4 2D DQF-COSY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
5	PCP7T	natural abundance	500 uM
6	TRIS	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

5 2D 1H-15N HSQC

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

6 2D 1H-13C HSQC

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

7 3D CBCA(CO)NH

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

8 3D HNCO

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

9 3D HNCA

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

10 3D HNCACB

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

11 3D HBHA(CO)NH

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

12 3D HN(CO)CA

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

13 3D HCCH-TOCSY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

14 3D HNCCCONH

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

15 3D CBCANH

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	PCP7T	[U-100% 13C; U-100% 15N]	300.0 ~ 500.0 uM
2	TRIS	natural abundance	50 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

16 2D 1H-1H TOCSY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
5	PCP7T	natural abundance	500 uM
6	TRIS	natural abundance	50 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

17 3D 1H-15N TOCSY

Instrument

Bruker Bruker - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	PCP7T	[U-100% 15N]	350.0 ~ 500.0 uM
10	TRIS	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25065_2mr8.nef
Input source #2: Coordindates	2mr8.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-
GAMAKAPESATEKVLCALYAEILGVERVGVDDAFHDLGGSSALAMRLIARIREELGVDLPIRQLFSSPTPAGVARALAAKSASWSHPQFEK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMAKAPESATEKVLCALYAEILGVERVGVDDAFHDLGGSSALAMRLIARIREELGVDLPIRQLFSSPTPAGVARALAAKSASWSHPQFEK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_25065_2mr8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	613		93.4 (chain: A, length: 91)
2	Assigned chemical shifts	assigned_chem_shift_list_1_2	Warning	459		90.1 (chain: A, length: 91)
3	Assigned chemical shifts	assigned_chem_shift_list_1_2_3	Warning	480		97.8 (chain: A, length: 91)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1161 (1)	noe	89.0 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 93.4%
- Total number of assignments
  - ¹H chemical shifts: 417
  - ¹³C chemical shifts: 196
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_1_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 90.1%
- Total number of assignments
  - ¹H chemical shifts: 385
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_1_2_3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 480
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	515	417	81.0
¹³C chemical shifts	397	196	49.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	152	82.6
¹³C chemical shifts	182	39	21.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	331	265	80.1
¹³C chemical shifts	215	157	73.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	57	95.0
¹³C chemical shifts	60	57	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	8	27.6
¹³C chemical shifts	28	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	515	385	74.8
¹⁵N chemical shifts	95	74	77.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	154	83.7
¹⁵N chemical shifts	86	71	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	331	231	69.8
¹⁵N chemical shifts	9	3	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	53	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	14	48.3
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	515	480	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	173	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	331	307	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	60	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 89.0%
- Total number of restraints: 1161
- Weight of restraints: 1.0 (1161)
- Potential type of restraints: square-well-parabolic (1161)
- Range of distance target values: 1.35, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Non-ribosomal peptide synthetase, peptidyl carrier protein

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Found 1 Document (0.691 seconds)

BMRB: 25065

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Related entities 1. PCP7T, : 1 : 1 : 123 entities Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 5 contents Detail