4KT7 | pdb_00004kt7

The crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548

PDB DOI: https://doi.org/10.2210/pdb4KT7/pdb

Classification: TRANSFERASE
Organism(s): Anaerococcus prevotii DSM 20548
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-20 Released: 2013-06-05
Deposition Author(s): Borek, D., Tan, K., Stols, L., Eschenfeidt, W.H., Otwinoski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4KT7

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548

Borek, D., Tan, K., Stols, L., Eschenfeidt, W.H., Otwinoski, Z., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 54.95 kDa
Atom Count: 3,893
Modeled Residue Count: 446
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	A, B	237	Anaerococcus prevotii DSM 20548	Mutation(s): 0 Gene Names: Apre_0175, ispD EC: 2.7.7.60
UniProt
Find proteins for C7RFG6 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7RFG6 Go to UniProtKB: C7RFG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7RFG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density 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: 2.00 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.858	α = 90
b = 145.509	β = 90
c = 36.719	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SBC-Collect	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Eschenfeidt, W.H.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, 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.