3KVP

Crystal Structure of Uncharacterized protein ymzC Precursor from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR378A

PDB DOI: https://doi.org/10.2210/pdb3KVP/pdb

Classification: structural genomics, unknown function
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-30 Released: 2010-02-02
Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Afonine, P., Fang, F., Xiao, R., Cunningham, K., Ma, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.237
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SR378A

Kuzin, A.P., Chen, Y., Afonine, P., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 52.17 kDa
Atom Count: 2,286
Modelled Residue Count: 265
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ymzC	A, B, C, D, E A, B, C, D, E, F	72	Bacillus subtilis	Mutation(s): 0 Gene Names: BSU17350, ymzC
UniProt
Find proteins for O31797 (Bacillus subtilis (strain 168)) Explore O31797 Go to UniProtKB: O31797
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O31797
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	G [auth B], H [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.237
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.39	α = 90
b = 66.39	β = 90
c = 175.573	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description

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Help and Resources

3KVP

Crystal Structure of Uncharacterized protein ymzC Precursor from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR378A

Northeast Structural Genomics Consortium Target SR378A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)