4N7T | pdb_00004n7t

Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb4N7T/pdb

Classification: ISOMERASE
Organism(s): Streptococcus mutans UA159
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-16 Released: 2013-11-06
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Bonanno, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans

Fedorov, A.A., Fedorov, E.V., Bonanno, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 91.48 kDa
Atom Count: 6,596
Modeled Residue Count: 803
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopentomutase	A, B	413	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: deoB, SMU_1233 EC: 5.4.2.7
UniProt
Find proteins for Q8DTU0 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTU0 Go to UniProtKB: Q8DTU0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DTU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, B	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203 (Depositor), 0.200 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.788	α = 90
b = 63.687	β = 98.85
c = 104.765	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 1.1: 2013-11-27
Changes: Structure summary
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary