2PIH | pdb_00002pih

Crystal structure of Protein ymcA from Bacillus subtilis, NorthEast Structural Genomics target SR375

PDB DOI: https://doi.org/10.2210/pdb2PIH/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-13 Released: 2007-05-01
Deposition Author(s): Seetharaman, J., Abashidze, M., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., 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: 2.10 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Protein ymcA from Bacillus subtilis.

Seetharaman, J., Abashidze, M., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 34.8 kDa
Atom Count: 2,179
Modeled Residue Count: 246
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ymcA	A, B	151	Bacillus subtilis	Mutation(s): 3 Gene Names: ymcA, BSU17020
UniProt
Find proteins for O31779 (Bacillus subtilis (strain 168)) Explore O31779 Go to UniProtKB: O31779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31779
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.322	α = 61.85
b = 52.201	β = 90.64
c = 55.448	γ = 90.01

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary