4KH8 | pdb_00004kh8

Crystal structure of a Lipocalin-like protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4KH8/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-30 Released: 2013-05-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of a hypothetical protein (EF0376) from Enterococcus faecalis V583 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2,931 
• Modeled Residue Count: 311 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A	318	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_0376, NP_814167.1
UniProt
Find proteins for Q838Q9 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838Q9  Go to UniProtKB:  Q838Q9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNL	B [auth A]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34KH8

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.745	α = 90
b = 99.745	β = 90
c = 56.956	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary