3FMC

CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.80 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3FMC/pdb

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

Deposited: 2008-12-19 Released: 2009-01-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.187
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative succinylglutamate desuccinylase / aspartoacylase (YP_926482.1) from Shewanella amazonensis SB2B at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 166.66 kDa
Atom Count: 13,752
Modelled Residue Count: 1,461
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative succinylglutamate desuccinylase / aspartoacylase	A, B, C, D	368	Shewanella amazonensis SB2B	Mutation(s): 0 Gene Names: Sama_0604, YP_926482.1
UniProt
Find proteins for A1S356 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S356 Go to UniProtKB: A1S356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1S356
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A], G [auth B], K [auth C], M [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] H [auth B] I [auth B] J [auth B] L [auth C] F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], O [auth D], P [auth D], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.187
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33FMC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.279	α = 90
b = 140.101	β = 90
c = 164.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-01-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-01-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

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3FMC

CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.80 A RESOLUTION

Crystal structure of putative succinylglutamate desuccinylase / aspartoacylase (YP_926482.1) from Shewanella amazonensis SB2B at 1.80 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)