3L39 | pdb_00003l39

Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L39/pdb

• Classification: phosphate-binding protein
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-16 Released: 2010-01-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 27.16 kDa 
• Atom Count: 2,008 
• Modeled Residue Count: 209 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative PhoU-like phosphate regulatory protein	A	227	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT4638, BT_4638
UniProt
Find proteins for Q89YU3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YU3  Go to UniProtKB:  Q89YU3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33L39

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.587	α = 90
b = 79.587	β = 90
c = 237.385	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description