8VVA | pdb_00008vva

Structure of DUF1480 domain-containing protein from Klebsiella pneumoniae subsp. pneumoniae SA1

PDB DOI: https://doi.org/10.2210/pdb8VVA/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-30 Released: 2024-06-19
Deposition Author(s): Semper, C., Savchenko, A., Watanabe, N., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.205 (Depositor), 0.206 (DCC)
R-Value Observed:
0.208 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Structure of DUF1480 domain-containing protein from Klebsiella pneumoniae subsp. pneumoniae SA1

Semper, C., Savchenko, A., Watanabe, N., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 18.22 kDa
Atom Count: 1,286
Modeled Residue Count: 154
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1480 domain-containing protein, YebV family	A, B	79	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: BB784_10290
UniProt
Find proteins for A0A6B2HLC6 (Klebsiella pneumoniae) Explore A0A6B2HLC6 Go to UniProtKB: A0A6B2HLC6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6B2HLC6
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: 1.75 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.205 (Depositor), 0.206 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.591	α = 90
b = 78.591	β = 90
c = 62.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.