3GA2 | pdb_00003ga2

Crystal structure of the Endonuclease_V (BSU36170) from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR624

PDB DOI: https://doi.org/10.2210/pdb3GA2/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-02-16 Released: 2009-02-24
Deposition Author(s): Forouhar, F., Abashidze, M., Hussain, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.243 (Depositor), 0.255 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Endonuclease_V (BSU36170) from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR624

Forouhar, F., Abashidze, M., Hussain, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 28.36 kDa
Atom Count: 2,049
Modeled Residue Count: 237
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease V	A	246	Bacillus subtilis	Mutation(s): 1 Gene Names: nfi, ywqL EC: 3.1.21.7
UniProt
Find proteins for P96724 (Bacillus subtilis (strain 168)) Explore P96724 Go to UniProtKB: P96724
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96724
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.243 (Depositor), 0.255 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.806	α = 90
b = 83.861	β = 90
c = 52.287	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SnB	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-02-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-02-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references, Source and taxonomy, Structure summary
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary