- PDB-1vp7: Crystal structure of Exodeoxyribonuclease VII small subunit (NP_8... -
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Open data
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Basic information
Entry
Database: PDB / ID: 1vp7
Title
Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution
Components
exodeoxyribonuclease VII small subunitExonuclease VII
Keywords
HYDROLASE / NP_881400.1 / Exodeoxyribonuclease VII small subunit E.C.3.1.11.6 / structural genomics / Joint Center for Structural Genomics / JCSG / PSI / Protein Structure Initiative
Function / homology
Function and homology information
exodeoxyribonuclease VII / exodeoxyribonuclease VII activity / exodeoxyribonuclease VII complex / DNA catabolic process / cytoplasm Similarity search - Function
Exonuclease VII, small subunit / Exonuclease VII, small subunit / Exonuclease VII, small subunit superfamily / Exonuclease VII small subunit / Helix Hairpins / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
A: exodeoxyribonuclease VII small subunit B: exodeoxyribonuclease VII small subunit C: exodeoxyribonuclease VII small subunit D: exodeoxyribonuclease VII small subunit E: exodeoxyribonuclease VII small subunit F: exodeoxyribonuclease VII small subunit
Resolution: 2.4→29.02 Å / Num. obs: 28264 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 42.73 Å2 / Rsym value: 0.13 / Net I/σ(I): 18
Reflection shell
Resolution: 2.4→2.53 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4033 / Rsym value: 0.616 / % possible all: 100
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Processing
Software
Name
Version
Classification
MOSFLM
datareduction
SCALA
5.0)
datascaling
SHELX
modelbuilding
autoSHARP
phasing
REFMAC
5.2.0005
refinement
CCP4
(SCALA)
datascaling
SHELX
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.4→29.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.479 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.208 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. DENSITY IS POOR FOR E78-79, F78-79, F33-36. 2. UNEXPLAINED DENSITIES: BETWEEN A20/B20; BETWEEN C20/D20; BETWEEN E20/F20; NEAR D80/D82 AND NEAR C12/C14/C30/C39.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2444
1388
4.9 %
RANDOM
Rwork
0.20268
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obs
0.20473
26875
99.88 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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