BMRBj - BMREntryMaster

Found 1 Document (0.691 seconds)

BMRB: 15442

2JUG

Multienzyme Docking in Hybrid Megasynthetases

Authors

Richter, C.D., Nietlispach, D., Broadhurst, R.W., Weissman, K.J.

Assembly

TubCdd dimer

Entity

1. TubCdd dimer (polymer, Thiol state: not present), 78 monomers, 8116.288 × 2 Da Detail

GPLGSSAGAL LAHAASLGVR LWVEGERLRF QAPPGVMTPE LQSRLGGARH ELIALLRQLQ PSSQGGSLLA PVARNGRL

Total weight

16232.576 Da

Max. entity weight

8116.288 Da

Source organism

Archangium disciforme

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.2 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (811 of 861)	94.2 % (423 of 449)	93.7 % (312 of 333)	96.2 % (76 of 79)
Backbone	95.8 % (437 of 456)	97.5 % (157 of 161)	94.6 % (211 of 223)	95.8 % (69 of 72)
Sidechain	93.2 % (440 of 472)	92.4 % (266 of 288)	94.4 % (167 of 177)	100.0 % (7 of 7)
Aromatic	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (14 of 14)	100.0 % (1 of 1)
Methyl	95.1 % (97 of 102)	96.1 % (49 of 51)	94.1 % (48 of 51)

1. TubCdd

GPLGSSAGAL LAHAASLGVR LWVEGERLRF QAPPGVMTPE LQSRLGGARH ELIALLRQLQ PSSQGGSLLA PVARNGRL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6, Details This was a mixed labelled sample of unlabelled and labelled protein prepared by mixing, thermal denaturation and refolding by cooling to room temperature

#	Name	Isotope labeling	Concentration
8	TubCdd	[U-100% 13C; U-100% 15N]	0.5 mM
9	TubCdd	natural abundance	0.5 mM
10	TSP	natural abundance	20 uM
11	sodium azide	natural abundance	0.1 %
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	100 mM
14	TubCdd	natural abundance	0.5 mM
15	H2O		90 %
16	D2O		10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbon	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	internal	indirect	0.1013291

Referencing offset: 0.26 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2JUG, Strand ID: A, B Detail

Release date

2007-08-23

Citation

Multienzyme docking in hybrid megasynthetases
Richter, C.D., Nietlispach, D., Broadhurst, R.W., Weissman, K.J.
Nat. Chem. Biol. (2008), 4, 75-81, PubMed 18066054 , DOI 10.1038/nchembio.2007.61 , Abstract

Related entities 1. TubCdd dimer, : 1 : 3 entities Detail

Experiments performed 11 experiments Detail

1 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

2 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

3 3D 13C-separated 12C-selected NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6, Details This was a mixed labelled sample of unlabelled and labelled protein prepared by mixing, thermal denaturation and refolding by cooling to room temperature

#	Name	Isotope labeling	Concentration
8	TubCdd	[U-100% 13C; U-100% 15N]	0.5 mM
9	TubCdd	natural abundance	0.5 mM
10	TSP	natural abundance	20 uM
11	sodium azide	natural abundance	0.1 %
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	100 mM
14	TubCdd	natural abundance	0.5 mM
15	H2O		90 %
16	D2O		10 %

4 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

5 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

6 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

7 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

8 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

9 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

10 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

11 3D 1H-15N TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6

#	Name	Isotope labeling	Concentration
1	TubCdd	[U-100% 13C; U-100% 15N]	1 mM
2	TSP	natural abundance	20 uM
3	sodium azide	natural abundance	0.1 %
4	sodium phosphate	natural abundance	50 mM
5	sodium chloride	natural abundance	100 mM
6	H2O		90 %
7	D2O		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15442_2jug.nef
Input source #2: Coordindates	2jug.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--------
GPLGSSAGALLAHAASLGVRLWVEGERLRFQAPPGVMTPELQSRLGGARHELIALLRQLQPSSQGGSLLAPVARNGRL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSSAGALLAHAASLGVRLWVEGERLRFQAPPGVMTPELQSRLGGARHELIALLRQLQPSSQGGSLLAPVARNGRL

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

--------10--------20--------30--------40--------50--------60--------70--------
GPLGSSAGALLAHAASLGVRLWVEGERLRFQAPPGVMTPELQSRLGGARHELIALLRQLQPSSQGGSLLAPVARNGRL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSSAGALLAHAASLGVRLWVEGERLRFQAPPGVMTPELQSRLGGARHELIALLRQLQPSSQGGSLLAPVARNGRL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0
B	B	78	0	0	100.0

Content subtype: combined_15442_2jug.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	804		100.0 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2112 (1)	noe	98.7 (chain: A, length: 78)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	40 (1)	hbond	39.7 (chain: A, length: 78)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	105 (104)	.	70.5 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 421
  - ¹³C chemical shifts: 308
  - ¹⁵N chemical shifts: 75
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
75	ASN	CG	177.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	449	417	92.9
¹³C chemical shifts	333	307	92.2
¹⁵N chemical shifts	87	75	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	156	96.9
¹³C chemical shifts	156	143	91.7
¹⁵N chemical shifts	72	68	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	261	90.6
¹³C chemical shifts	177	164	92.7
¹⁵N chemical shifts	15	7	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	49	94.2
¹³C chemical shifts	52	48	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	14	14	100.0
¹⁵N chemical shifts	1	1	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: 78, Sequence coverage: 98.7%
- Total number of restraints: 2074
- Weight of restraints: 1.0 (2074)
- Potential type of restraints: square-well-parabolic (2074)
- Range of distance target values: 1.75, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 39.7%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 70.5%
- Total number of restraints: 104
- Total number of restraints per polymer type: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: square-well-parabolic (104)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dimer, docking domain, nonribosomal peptide synthetase, tubulysin

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.691 seconds)

BMRB: 15442

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TubCdd dimer, : 1 : 3 entities Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail