2D4W | pdb_00002d4w

Crystal structure of glycerol kinase from Cellulomonas sp. NT3060

PDB DOI: https://doi.org/10.2210/pdb2D4W/pdb

Classification: TRANSFERASE
Organism(s): Cellulomonas sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-10-24 Released: 2006-11-14
Deposition Author(s): Imada, K., Tamura, T., Namba, K., Inagaki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of glycerol kinase from Cellulomonas sp. NT3060

Imada, K., Tamura, T., Inagaki, K.

To be published.

Macromolecule Content

Total Structure Weight: 110.86 kDa
Atom Count: 8,139
Modeled Residue Count: 1,006
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B	504	Cellulomonas sp.	Mutation(s): 0 EC: 2.7.1.30

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240 (Depositor), 0.242 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.43	α = 90
b = 105.43	β = 90
c = 195.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations