4E69 | pdb_00004e69

Crystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus, unliganded structure

PDB DOI: https://doi.org/10.2210/pdb4E69/pdb

Classification: TRANSFERASE
Organism(s): Oceanicola granulosus HTCC2516
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-15 Released: 2012-04-18
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.197 (Depositor), 0.194 (DCC)
R-Value Work:
0.168 (Depositor), 0.164 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus, unliganded structure

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 69.81 kDa
Atom Count: 5,522
Modeled Residue Count: 621
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxygluconokinase	A, B	328	Oceanicola granulosus HTCC2516	Mutation(s): 0 Gene Names: OG2516_05533
UniProt
Find proteins for Q2CIP5 (Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516)) Explore Q2CIP5 Go to UniProtKB: Q2CIP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2CIP5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] J [auth B] C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.197 (Depositor), 0.194 (DCC)
R-Value Work: 0.168 (Depositor), 0.164 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.249	α = 90
b = 76.306	β = 105.8
c = 76.245	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description