3I0Z | pdb_00003i0z

Crystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3I0Z/pdb

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-25 Released: 2009-07-14
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.178 (Depositor), 0.185 (DCC)
R-Value Work:
0.139 (Depositor), 0.149 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 87.98 kDa
Atom Count: 7,105
Modeled Residue Count: 776
Deposited Residue Count: 778
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 tagatose-6-phosphate ketose/aldose isomerase	A, B	389	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: agaS, NP_344614.1, SP_0065
UniProt
Find proteins for A0A0H2UN25 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UN25 Go to UniProtKB: A0A0H2UN25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UN25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] 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 N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] 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 N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.178 (Depositor), 0.185 (DCC)
R-Value Work: 0.139 (Depositor), 0.149 (DCC)
R-Value Observed: 0.141 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33I0Z

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.635	α = 90
b = 111.267	β = 97.09
c = 126.6	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: 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: 2024-11-20
Changes: Data collection, Structure summary