2CZ8 | pdb_00002cz8

Crystal Structure of tt0972 protein from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb2CZ8/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-07-11 Released: 2006-09-19
Deposition Author(s): Kumei, M., Inagaki, E., Nakano, N., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.229 (Depositor), 0.237 (DCC)
R-Value Work:
0.205 (Depositor), 0.214 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

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 tt0972 protein from Thermus thermophilus

Kumei, M., Inagaki, E., Nakano, N., Shinkai, A., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 69.37 kDa
Atom Count: 5,584
Modeled Residue Count: 537
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tt0972 protein	A, B, C, D, E A, B, C, D, E, F, G, H	69	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIE3 Go to UniProtKB: Q5SIE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth H]	CA [auth H] K [auth A] M [auth B] O [auth C] R [auth D] CA [auth H], K [auth A], M [auth B], O [auth C], R [auth D], U [auth E], W [auth F], Z [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain BA [auth H] SDF format, chain AA [auth H] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] I [auth A] L [auth B] P [auth D] AA [auth H], BA [auth H], I [auth A], L [auth B], P [auth D], Q [auth D], S [auth E], V [auth F], X [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain T [auth E] SDF format, chain N [auth C] SDF format, chain J [auth A] MOL2 format, chain Y [auth G] MOL2 format, chain T [auth E] MOL2 format, chain N [auth C] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth G] mmCIF format, chain T [auth E] mmCIF format, chain N [auth C] mmCIF format, chain J [auth A]	J [auth A], N [auth C], T [auth E], Y [auth G]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C] Focus chain T [auth E] Focus chain Y [auth G] Interactions & Density Focus chain J [auth A] Focus chain N [auth C] Focus chain T [auth E] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.229 (Depositor), 0.237 (DCC)
R-Value Work: 0.205 (Depositor), 0.214 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.36	α = 90
b = 66.36	β = 90
c = 124.566	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-09-19

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-09-19
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description