4KH9

Crystal structure of a DUF4785 family protein (lpg0956) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4KH9/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-30 Released: 2013-07-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6K9O

Literature

Crystal structure of a hypothetical protein (lpg0956) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.00 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.73 kDa 
• Atom Count: 6,077 
• Modelled Residue Count: 721 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	374	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: lpg0956, YP_094990.1
UniProt
Find proteins for Q5ZWX8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWX8  Go to UniProtKB:  Q5ZWX8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	C [auth A], D [auth B], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M34KH9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.807	α = 64.13
b = 62.975	β = 82.94
c = 70.632	γ = 67.17

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

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-07-03
  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