2I52 | pdb_00002i52

Crystal structure of protein PTO0218 from Picrophilus torridus, Pfam DUF372

PDB DOI: https://doi.org/10.2210/pdb2I52/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Picrophilus oshimae DSM 9789
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-08-23 Released: 2006-09-12
Deposition Author(s): Ramagopal, U.A., Gilmore, J., Toro, R., Bain, K.T., McKenzie, C., Reyes, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structure of hypothetical protein PTO0218 from Picrophilus torridus

Ramagopal, U.A., Gilmore, J., Toro, R., Bain, K.T., McKenzie, C., Reyes, C., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 83.53 kDa
Atom Count: 6,469
Modeled Residue Count: 697
Deposited Residue Count: 726
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D, E A, B, C, D, E, F	121	Picrophilus oshimae DSM 9789	Mutation(s): 0 EC: 4.1.2.25
UniProt
Find proteins for Q6L2J9 (Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / KAW 2/3)) Explore Q6L2J9 Go to UniProtKB: Q6L2J9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6L2J9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain W [auth F] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain W [auth F] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain W [auth F]	O [auth D], P [auth D], Q [auth D], W [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth F] Interactions & Density Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain W [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F]	G [auth A] H [auth B] I [auth B] J [auth B] L [auth C] G [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth D], R [auth E], S [auth E], T [auth E], U [auth E], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.764	α = 90
b = 143.485	β = 90
c = 129.799	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-09-12

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-09-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-02-21
Changes: Data collection, Database references