2ANU | pdb_00002anu

Crystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb2ANU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-08-11 Released: 2005-10-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.220 (Depositor), 0.196 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 184.5 kDa
Atom Count: 11,171
Modeled Residue Count: 1,334
Deposited Residue Count: 1,530
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM0559	A, B, C, D, E A, B, C, D, E, F	255	Thermotoga maritima MSB8	Mutation(s): 6 Gene Names: tm0559
UniProt
Find proteins for Q9WZ29 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ29 Go to UniProtKB: Q9WZ29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZ29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain T [auth C] SDF format, chain QA [auth F] SDF format, chain PA [auth F] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth E] SDF format, chain G [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth C] MOL2 format, chain QA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth C] mmCIF format, chain QA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain G [auth A]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] G [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], N [auth B], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], T [auth C], U [auth C], V [auth C], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain LA [auth E] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A]	EA [auth D] FA [auth D] K [auth A] KA [auth E] L [auth A] EA [auth D], FA [auth D], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], R [auth B], RA [auth F], S [auth B], SA [auth F], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.220 (Depositor), 0.196 (DCC)
R-Value Work: 0.169 (Depositor), 0.180 (DCC)

Diffraction Data:

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.307	α = 90
b = 111.307	β = 90
c = 383.222	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXE	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-10-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-10-18
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary