3T80 | pdb_00003t80

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

PDB DOI: https://doi.org/10.2210/pdb3T80/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-31 Released: 2011-09-14
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Staker, B.L., Edwards, T.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.245 (Depositor), 0.224 (DCC)
R-Value Work:
0.211 (Depositor), 0.196 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Staker, B.L., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 106.44 kDa
Atom Count: 6,999
Modeled Residue Count: 915
Deposited Residue Count: 972
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, B, C, D, E A, B, C, D, E, F	162	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: ispF, STM2929 EC: 4.6.1.12
UniProt
Find proteins for Q8ZMF7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMF7 Go to UniProtKB: Q8ZMF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZMF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTN Query on CTN Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain NA [auth F] SDF format, chain Q [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C]	DA [auth D] IA [auth E] J [auth A] NA [auth F] Q [auth B] DA [auth D], IA [auth E], J [auth A], NA [auth F], Q [auth B], X [auth C]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain DA [auth D] Focus chain IA [auth E] Focus chain J [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain IA [auth E] Focus chain J [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain X [auth C]
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A]	JA [auth E], K [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain JA [auth E] Focus chain K [auth A] Interactions & Density Focus chain JA [auth E] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain LA [auth F] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	AA [auth D] G [auth A] GA [auth E] LA [auth F] O [auth B] AA [auth D], G [auth A], GA [auth E], LA [auth F], O [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain O [auth B] Focus chain V [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	EA [auth D] FA [auth D] KA [auth E] L [auth A] M [auth A] EA [auth D], FA [auth D], KA [auth E], L [auth A], M [auth A], N [auth A], OA [auth F], PA [auth F], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain MA [auth F] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	BA [auth D] CA [auth D] H [auth A] HA [auth E] I [auth A] BA [auth D], CA [auth D], H [auth A], HA [auth E], I [auth A], MA [auth F], P [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain P [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.245 (Depositor), 0.224 (DCC)
R-Value Work: 0.211 (Depositor), 0.196 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.013	α = 90
b = 147.657	β = 106.38
c = 56.919	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Staker, B.L.

Edwards, T.E.

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2011-10-12
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description