4HWM | pdb_00004hwm

Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution

PDB DOI: https://doi.org/10.2210/pdb4HWM/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-08 Released: 2013-01-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.179 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.160 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 14.45 kDa
Atom Count: 1,156
Modeled Residue Count: 117
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein yedD	A	130	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: yedD, KPN78578_23820, KPN_02420
UniProt
Find proteins for A6TB72 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TB72 Go to UniProtKB: A6TB72
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TB72
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.38 Å
R-Value Free: 0.179 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.160 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34HWM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.81	α = 90
b = 51.067	β = 90
c = 52.436	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-02-01
Changes: Database references, Derived calculations
Version 1.3: 2024-10-09
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.