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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.166 (Depositor), 0.172 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3L39

This is version 1.5 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89YU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.202 (Depositor), 0.203 (DCC)
R-Value Work: 0.166 (Depositor), 0.172 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

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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.