5CAI | pdb_00005cai

Crystal structure of a putative lipoprotein from the DUF903 family (KPN_03160) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5CAI/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-29 Released: 2015-07-22 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of a putative lipoprotein from the DUF903 family (KPN_03160) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.32 kDa 
• Atom Count: 2,860 
• Modeled Residue Count: 316 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein from the DUF903 family	A, B, C, D, E, F	56	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: ygdI, YP_001336791.1
UniProt
Find proteins for A6TD90 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TD90  Go to UniProtKB:  A6TD90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	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: 2.30 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35CAI

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.21	α = 90
b = 108.21	β = 90
c = 142.19	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2023-02-01
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Structure summary