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BMRB: 17151

2L2S

Solution structure of peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with 1-{[(4-methylphenyl)thio]acetyl}piperidine. Seattle Structure Genomics Center for Infectious Disease (SSGCID)

Authors

Zheng, S., Barnwal, R., Leeper, T., Varani, G.

Assembly

FKBP in complex with 1-{[(4-methylphenyl)thio]acetyl}piperidine

Entity

1. FKBP (polymer, Thiol state: all free), 117 monomers, 12228.61 Da Detail

GPGSMTVVTT ESGLKYEDLT EGSGAEARAG QTVSVHYTGW LTDGQKFDSS KDRNDPFAFV LGGGMVIKGW DEGVQGMKVG GVRRLTIPPQ LGYGARGAGG VIPPNATLVF EVELLDV

2. 1-{[(4-methylphenyl)thio]acetyl}piperidine (non-polymer, Thiol state: all disulfide bound), na Da

Formula weight

12228.61 Da

Source organism

Burkholderia pseudomallei

Exptl. method

solution NMR

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 87.0 %, Completeness (bb): 82.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.0 % (1104 of 1269)	93.9 % (611 of 651)	75.6 % (377 of 499)	97.5 % (116 of 119)
Backbone	82.2 % (567 of 690)	96.4 % (240 of 249)	66.1 % (218 of 330)	98.2 % (109 of 111)
Sidechain	93.5 % (631 of 675)	92.3 % (371 of 402)	95.5 % (253 of 265)	87.5 % (7 of 8)
Aromatic	95.7 % (88 of 92)	97.8 % (45 of 46)	95.5 % (42 of 44)	50.0 % (1 of 2)
Methyl	98.5 % (130 of 132)	98.5 % (65 of 66)	98.5 % (65 of 66)

1. FKBP

GPGSMTVVTT ESGLKYEDLT EGSGAEARAG QTVSVHYTGW LTDGQKFDSS KDRNDPFAFV LGGGMVIKGW DEGVQGMKVG GVRRLTIPPQ LGYGARGAGG VIPPNATLVF EVELLDV

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	DSS	methyl protons	4.71 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	DSS	methyl protons	4.71 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	DSS	methyl protons	4.71 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L2S, Strand ID: A Detail

Release date

2010-10-31

Related entities 1. FKBP, : 1 : 2 : 14 : 291 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

2 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

3 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

10 3D 1H-15N TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	KCl	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	DTT	natural abundance	1 mM

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
7	isomerase	[U-99% 13C; U-99% 15N]	0.6 ~ 1.5 mM
8	D2O	natural abundance	100 %
9	KCl	natural abundance	100 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17151_2l2s.nef
Input source #2: Coordindates	2l2s.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	L2S	1-{[(4-methylphenyl)sulfanyl]acetyl}piperidine	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GPGSMTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGG

-------110-------
VIPPNATLVFEVELLDV
|||||||||||||||||
VIPPNATLVFEVELLDV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0

Content subtype: combined_17151_2l2s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1116		98.3 (chain: A, length: 117), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2431 (1)	noe	95.7 (chain: A, length: 117)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	402 (402)	.	70.9 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 98.3%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 637
  - ¹⁵N chemical shifts: 116
  - ¹³C chemical shifts: 363
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	651	622	95.5
¹⁵N chemical shifts	124	116	93.5
¹³C chemical shifts	499	363	72.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	249	244	98.0
¹⁵N chemical shifts	111	109	98.2
¹³C chemical shifts	234	112	47.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	402	378	94.0
¹⁵N chemical shifts	13	7	53.8
¹³C chemical shifts	265	251	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	66	95.7
¹³C chemical shifts	69	65	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	44	95.7
¹⁵N chemical shifts	2	1	50.0
¹³C chemical shifts	44	40	90.9

Comp_index_ID	Comp_ID
1	L2S

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 95.7%
- Total number of restraints: 2431
- Weight of restraints: 1.0 (2431)
- Potential type of restraints: upper-bound-parabolic (2431)
- Range of distance target values: 2.58, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 70.9%
- Total number of restraints: 402
- Total number of restraints per polymer type: 402
- Weight of restraints: 1.0 (402)
- Potential type of restraints: square-well-parabolic (402)
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cis-trans isomerase, complex, FKBP, NMR

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Found 1 Document (0.756 seconds)

BMRB: 17151

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. FKBP, : 1 : 2 : 14 : 291 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail