3F6M | pdb_00003f6m

Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3F6M/pdb

Classification: LYASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-06 Released: 2008-11-25
Deposition Author(s): Kim, Y., Maltseva, N., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.203 (Depositor), 0.197 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3F6M

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

Literature

Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis

Kim, Y., Maltseva, N., Stam, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 17.66 kDa
Atom Count: 1,242
Modeled Residue Count: 161
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A	165	Yersinia pestis CO92	Mutation(s): 0 Gene Names: ispF, y0829, YPO3360, YP_0327 EC: 4.6.1.12
UniProt
Find proteins for Q8ZBP7 (Yersinia pestis) Explore Q8ZBP7 Go to UniProtKB: Q8ZBP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZBP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.203 (Depositor), 0.197 (DCC)
R-Value Work: 0.194 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.64	α = 90
b = 146.64	β = 90
c = 146.64	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-11-06
Changes: 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.