7KMW | pdb_00007kmw

Crystal structure of IspD from Mycobacterium paratuberculosis

PDB DOI: https://doi.org/10.2210/pdb7KMW/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium avium subsp. paratuberculosis K-10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-03 Released: 2020-11-11
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.223 (Depositor), 0.225 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of IspD from Mycobacterium paratuberculosis

Pierce, P.G., Bolejack, M.J., Yano, J.K., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 105.64 kDa
Atom Count: 6,309
Modeled Residue Count: 856
Deposited Residue Count: 1,028
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 4-phosphate cytidylyltransferase	A, B, C, D	257	Mycobacterium avium subsp. paratuberculosis K-10	Mutation(s): 0 Gene Names: ispD, MAP_0476 EC: 2.7.7.60
UniProt
Find proteins for Q743W5 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q743W5 Go to UniProtKB: Q743W5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q743W5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.223 (Depositor), 0.225 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.13	α = 90
b = 45.62	β = 126.75
c = 121.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2021-07-21
Changes: Other, Structure summary
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description