3TEV | pdb_00003tev

The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1

PDB DOI: https://doi.org/10.2210/pdb3TEV/pdb

Classification: HYDROLASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-15 Released: 2011-08-31
Deposition Author(s): Chang, C., Hatzos-Skintges, C., Kohler, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3TEV

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of glycosyl hydrolase from Deinococcus radiodurans R1

Chang, C., Hatzos-Skintges, C., Kohler, M., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.14 kDa
Atom Count: 4,984
Modeled Residue Count: 626
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hyrolase, family 3	A, B	351	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: DR_1333
UniProt
Find proteins for Q9RUP9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUP9 Go to UniProtKB: Q9RUP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RUP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.841	α = 90
b = 146.841	β = 90
c = 108.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Hatzos-Skintges, C.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, 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.