2HF1 | pdb_00002hf1

Crystal structure of the putative Tetraacyldisaccharide-1-P 4-kinase from Chromobacterium violaceum. NESG target CvR39.

PDB DOI: https://doi.org/10.2210/pdb2HF1/pdb

Classification: TRANSFERASE
Organism(s): Chromobacterium violaceum ATCC 12472
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-06-22 Released: 2006-08-22
Deposition Author(s): Vorobiev, S.M., Abashidze, M., Seetharaman, J., Chen, C.X., Jiang, M., Cunningham, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.284 (Depositor), 0.303 (DCC)
R-Value Work:
0.233 (Depositor), 0.246 (DCC)
R-Value Observed:
0.233 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the putative Tetraacyldisaccharide-1-P 4-kinase from Chromobacterium violaceum.

Vorobiev, S.M., Abashidze, M., Seetharaman, J., Chen, C.X., Jiang, M., Cunningham, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 16.07 kDa
Atom Count: 979
Modeled Residue Count: 120
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetraacyldisaccharide-1-P 4-kinase	A, B	68	Chromobacterium violaceum ATCC 12472	Mutation(s): 3 Gene Names: CV_3345 EC: 2.7.1.130
UniProt
Find proteins for Q7NSS5 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NSS5 Go to UniProtKB: Q7NSS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NSS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 1.90 Å
R-Value Free: 0.284 (Depositor), 0.303 (DCC)
R-Value Work: 0.233 (Depositor), 0.246 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.517	α = 90
b = 93.854	β = 90
c = 87.219	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SnB	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-08-22

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-08-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Data collection, Refinement description
Version 1.4: 2018-01-24
Changes: Database references
Version 1.5: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary