3M1T | pdb_00003m1t

Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution

PDB DOI: https://doi.org/10.2210/pdb3M1T/pdb

Classification: HYDROLASE
Organism(s): Shewanella amazonensis SB2B
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-05 Released: 2010-03-31
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.201 (Depositor), 0.225 (DCC)
R-Value Work:
0.182 (Depositor), 0.204 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3M1T

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

Literature

Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 29.96 kDa
Atom Count: 2,469
Modeled Residue Count: 269
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphohydrolase	A	275	Shewanella amazonensis SB2B	Mutation(s): 0 Gene Names: Sama_3455
UniProt
Find proteins for A1SBA1 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1SBA1 Go to UniProtKB: A1SBA1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1SBA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.201 (Depositor), 0.225 (DCC)
R-Value Work: 0.182 (Depositor), 0.204 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.729	α = 90
b = 69.729	β = 90
c = 124.569	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.