1VKD | pdb_00001vkd

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VKD/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-05-12 Released: 2004-05-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VKD

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

Literature

Crystal structure of hypothetical protein (TM1225) from Thermotoga maritima at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 234.21 kDa
Atom Count: 16,823
Modeled Residue Count: 1,956
Deposited Residue Count: 2,028
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein TM1225	A, B, C, D, E A, B, C, D, E, F	338	Thermotoga maritima MSB8	Mutation(s): 5 Gene Names: TM1225
UniProt
Find proteins for Q9X0V2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0V2 Go to UniProtKB: Q9X0V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0V2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth A]	G [auth A], H [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth D]

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: 2.10 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.867	α = 90
b = 100.908	β = 90
c = 253.433	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-05-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-05-25
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.