3H6E | pdb_00003h6e

The crystal structure of a carbohydrate kinase from Novosphingobium aromaticivorans

PDB DOI: https://doi.org/10.2210/pdb3H6E/pdb

Classification: TRANSFERASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-04-23 Released: 2009-06-02
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.274 (Depositor), 0.215 (DCC)
R-Value Work:
0.220 (Depositor), 0.216 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of carbohydrate kinase from Novosphingobium aromaticivorans

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 106.63 kDa
Atom Count: 7,469
Modeled Residue Count: 925
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate kinase, FGGY	A, B	482	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_1051
UniProt
Find proteins for Q2G9H7 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2G9H7 Go to UniProtKB: Q2G9H7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G9H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.50 Å
R-Value Free: 0.274 (Depositor), 0.215 (DCC)
R-Value Work: 0.220 (Depositor), 0.216 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.614	α = 90
b = 81.198	β = 90
c = 229.134	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Structure summary

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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.