2IDE

Crystal Structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2IDE/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-09-15 Released: 2007-09-25
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.226 (Depositor), 0.200 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (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 the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8

Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Baba, S., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 204.5 kDa
Atom Count: 14,850
Modelled Residue Count: 1,769
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum cofactor biosynthesis protein C	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	157	Thermus thermophilus HB8	Mutation(s): 0 EC: 4.6.1.17
UniProt
Find proteins for Q5SHE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHE1 Go to UniProtKB: Q5SHE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SHE1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth H] SDF format, chain V [auth I] SDF format, chain W [auth J] SDF format, chain X [auth K] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth I] MOL2 format, chain W [auth J] MOL2 format, chain X [auth K] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H] mmCIF format, chain V [auth I] mmCIF format, chain W [auth J] mmCIF format, chain X [auth K]	M [auth A] N [auth A] O [auth C] P [auth C] Q [auth E] M [auth A], N [auth A], O [auth C], P [auth C], Q [auth E], R [auth E], S [auth G], T [auth G], U [auth H], V [auth I], W [auth J], X [auth K]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226 (Depositor), 0.200 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.809	α = 90
b = 109.836	β = 104.86
c = 115.192	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Refinement description