2WYR | pdb_00002wyr

3-D structure of PhTET1-12s, dodecamer in the asymmetric unit

PDB DOI: https://doi.org/10.2210/pdb2WYR/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-20 Released: 2010-12-01
Deposition Author(s): Vellieux, F.M.D., Dura, M.A., Franzetti, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of Phtet1-12S, Dodecamer in the Asymmetric Unit

Dura, M.A., Vellieux, F.M.D.

To be published.

Macromolecule Content

Total Structure Weight: 445.09 kDa
Atom Count: 32,303
Modeled Residue Count: 3,904
Deposited Residue Count: 3,984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COBALT-ACTIVATED PEPTIDASE TET1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	332	Pyrococcus horikoshii OT3	Mutation(s): 0 EC: 3.4.11
UniProt
Find proteins for O58255 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58255 Go to UniProtKB: O58255
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain JA [auth L] SDF format, chain IA [auth L] SDF format, chain HA [auth K] SDF format, chain GA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth J] SDF format, chain DA [auth I] SDF format, chain CA [auth I] SDF format, chain BA [auth H] SDF format, chain AA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain IA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain IA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] CA [auth I] DA [auth I] EA [auth J] AA [auth H], BA [auth H], CA [auth I], DA [auth I], EA [auth J], FA [auth J], GA [auth K], HA [auth K], IA [auth L], JA [auth L], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth G], Z [auth G]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.263	α = 90
b = 205.218	β = 100.78
c = 113.488	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
TRUNCATE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Vellieux, F.M.D.

Dura, M.A.

Franzetti, B.

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary