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Found 1 Document (0.902 seconds)

BMRB: 16098

2KCW

Solution structure of Apo-form YjaB from Escherichia coli

Authors

Lu, J., Wang, X., Jin, C.

Assembly

Apo-form YjaB

Entity

1. Apo-form YjaB (polymer, Thiol state: all free), 147 monomers, 16446.49 Da Detail

MVISIRRSRH EEGEELVAIW CRSVDATHDF LSAEYRTELE DLVRSFLPEA PLWVAVNERD QPVGFMLLSG QHMDALFIDP DVRGCGVGRV LVEHALSMAP ELTTNVNEQN EQAVGFYKKV GFKVTGRSEV DDLGKPYPLL NLAYVGA

Formula weight

16446.49 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

MOLECULAR DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.2 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (1589 of 1686)	94.9 % (826 of 870)	93.4 % (621 of 665)	94.0 % (142 of 151)
Backbone	97.1 % (843 of 868)	98.0 % (292 of 298)	97.4 % (419 of 430)	94.3 % (132 of 140)
Sidechain	92.3 % (881 of 954)	93.4 % (534 of 572)	90.8 % (337 of 371)	90.9 % (10 of 11)
Aromatic	56.1 % (74 of 132)	63.6 % (42 of 66)	48.4 % (31 of 64)	50.0 % (1 of 2)
Methyl	98.9 % (178 of 180)	97.8 % (88 of 90)	100.0 % (90 of 90)

1. Apo-form YjaB

MVISIRRSRH EEGEELVAIW CRSVDATHDF LSAEYRTELE DLVRSFLPEA PLWVAVNERD QPVGFMLLSG QHMDALFIDP DVRGCGVGRV LVEHALSMAP ELTTNVNEQN EQAVGFYKKV GFKVTGRSEV DDLGKPYPLL NLAYVGA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	30 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	10 mM
4	YjaB protein	[U-13C; U-15N]	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.21 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: -0.21 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: -0.23 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.22 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 2KCW, Strand ID: A Detail

Release date

2009-04-16

Citation

Solution structure of Apo-YjaB from Escherichia coli
Lu, J., Wang, X., Xia, B., Jin, C.
Proteins (2009), 76, 261-265, PubMed 19343803 , DOI 10.1002/prot.22407 , Abstract

Related entities 1. Apo-form YjaB, : 1 : 2 : 23 entities Detail

Interaction partners 1. Apo-form YjaB, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16098_2kcw.nef
Input source #2: Coordindates	2kcw.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-------100
MVISIRRSRHEEGEELVAIWCRSVDATHDFLSAEYRTELEDLVRSFLPEAPLWVAVNERDQPVGFMLLSGQHMDALFIDPDVRGCGVGRVLVEHALSMAP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVISIRRSRHEEGEELVAIWCRSVDATHDFLSAEYRTELEDLVRSFLPEAPLWVAVNERDQPVGFMLLSGQHMDALFIDPDVRGCGVGRVLVEHALSMAP

-------110-------120-------130-------140-------
ELTTNVNEQNEQAVGFYKKVGFKVTGRSEVDDLGKPYPLLNLAYVGA
|||||||||||||||||||||||||||||||||||||||||||||||
ELTTNVNEQNEQAVGFYKKVGFKVTGRSEVDDLGKPYPLLNLAYVGA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	147	0	0	100.0

Content subtype: combined_16098_2kcw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1593		100.0 (chain: A, length: 147)
1	Distance restraints	AMBER_distance_constraints_3	Warning	231 (1)	noe	21.8 (chain: A, length: 147)
2	Distance restraints	AMBER_distance_constraints_6	Warning	14294 (1)	noe	99.3 (chain: A, length: 147)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	151 (151)	.	81.0 (chain: A, length: 147)
2	Dihedral angle restraints	AMBER_dihedral_5	Warning	1 (1)	.	1.4 (chain: A, length: 147)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 825
  - ¹³C chemical shifts: 622
  - ¹⁵N chemical shifts: 146
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
6	ARG	HH11	6.11
38	GLU	CD	179.78
71	GLN	CD	179.461
72	HIS	HE2	7.55

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	870	823	94.6
¹³C chemical shifts	665	620	93.2
¹⁵N chemical shifts	161	146	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	292	98.0
¹³C chemical shifts	294	284	96.6
¹⁵N chemical shifts	140	131	93.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	572	531	92.8
¹³C chemical shifts	371	336	90.6
¹⁵N chemical shifts	21	15	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	94	100.0
¹³C chemical shifts	94	94	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	37	56.1
¹³C chemical shifts	64	29	45.3
¹⁵N chemical shifts	2	1	50.0

Distance restraints

Saveframe: AMBER_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 21.8%
- Total number of restraints: 231
- Weight of restraints: 1.0 (231)
- Potential type of restraints: square-well-parabolic (231)
- Range of distance target values: 3.48, 7.22 (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
- Saveframe: AMBER_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 99.3%
  - Total number of restraints: 13903
  - Weight of restraints: 1.0 (13903)
  - Potential type of restraints: square-well-parabolic (13903)
  - Range of distance target values: 2.67, 8.08 (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

Dihedral angle restraints

Saveframe: AMBER_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 81.0%
- Total number of restraints: 151
- Total number of restraints per polymer type: 151
- Weight of restraints: 1.0 (151)
- Potential type of restraints: square-well-parabolic (151)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_5
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 147, Sequence coverage: 1.4%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

Keywords GNAT fold

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Found 1 Document (0.902 seconds)

BMRB: 16098

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Apo-form YjaB, : 1 : 2 : 23 entities Detail

Interaction partners 1. Apo-form YjaB, : 1 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail