4R4G

Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution

PDB DOI: https://doi.org/10.2210/pdb4R4G/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-19 Released: 2014-09-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.239
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 36.87 kDa
Atom Count: 2,584
Modelled Residue Count: 322
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative lipoprotein YcdA	A	326	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: ycdA, BSU02780
UniProt
Find proteins for O34538 (Bacillus subtilis (strain 168)) Explore O34538 Go to UniProtKB: O34538
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34538
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.239
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 6₅ 2 2
Diffraction Data: https://doi.org/10.18430/M34R4G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.653	α = 90
b = 98.653	β = 90
c = 195.018	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-11-27
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.