3FPI | pdb_00003fpi

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

PDB DOI: https://doi.org/10.2210/pdb3FPI/pdb

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

Deposited: 2009-01-05 Released: 2009-02-03
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: 2.80 Å
R-Value Free:
0.199 (Depositor), 0.167 (DCC)
R-Value Work:
0.170 (Depositor)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

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

To be published.

Macromolecule Content

Total Structure Weight: 18.57 kDa
Atom Count: 1,341
Modeled Residue Count: 161
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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| 3D Structure

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, YPTB0771, 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

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP Query on CTP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EPE Query on EPE 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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

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: 2.80 Å
R-Value Free: 0.199 (Depositor), 0.167 (DCC)
R-Value Work: 0.170 (Depositor)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.639	α = 90
b = 145.639	β = 90
c = 145.639	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
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-22
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary