2GO7 | pdb_00002go7

CRYSTAL STRUCTURE OF A HYDROLASE FROM HALOACID DEHALOGENASE-LIKE FAMILY (SP_2064) FROM STREPTOCOCCUS PNEUMONIAE TIGR4 AT 2.10 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2GO7/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-12 Released: 2006-05-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of (np_346487.1) from Streptococcus pneumoniae TIGR4 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 95.24 kDa
Atom Count: 7,025
Modeled Residue Count: 814
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrolase, haloacid dehalogenase-like family	A, B, C, D	207	Streptococcus pneumoniae TIGR4	Mutation(s): 2 Gene Names: np_346487.1
UniProt
Find proteins for A0A0H2URV7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URV7 Go to UniProtKB: A0A0H2URV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2URV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	E [auth A], K [auth B], N [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [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: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.171 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32GO7

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155	α = 90
b = 155	β = 90
c = 88.44	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-05-23
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

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Deposit Data

Help and Resources

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CRYSTAL STRUCTURE OF A HYDROLASE FROM HALOACID DEHALOGENASE-LIKE FAMILY (SP_2064) FROM STREPTOCOCCUS PNEUMONIAE TIGR4 AT 2.10 A RESOLUTION

Crystal structure of (np_346487.1) from Streptococcus pneumoniae TIGR4 at 2.10 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

2GO7 | pdb_00002go7