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- PDB-1vp7: Crystal structure of Exodeoxyribonuclease VII small subunit (NP_8... -

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Basic information

Entry
Database: PDB / ID: 1vp7
TitleCrystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution
Componentsexodeoxyribonuclease VII small subunitExonuclease VII
KeywordsHYDROLASE / 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
Exodeoxyribonuclease 7 small subunit / Exodeoxyribonuclease 7 small subunit
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Exodeoxyribonuclease VII small subunit E.C.3.1.11.6 (NP_881400.1) from Bordetella pertussis at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)67,3926
Polymers67,3926
Non-polymers00
Water2,396133
1
A: exodeoxyribonuclease VII small subunit
B: exodeoxyribonuclease VII small subunit


Theoretical massNumber of molelcules
Total (without water)22,4642
Polymers22,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-30 kcal/mol
Surface area9130 Å2
MethodPISA
2
C: exodeoxyribonuclease VII small subunit
D: exodeoxyribonuclease VII small subunit


Theoretical massNumber of molelcules
Total (without water)22,4642
Polymers22,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-25 kcal/mol
Surface area8800 Å2
MethodPISA
3
E: exodeoxyribonuclease VII small subunit
F: exodeoxyribonuclease VII small subunit


Theoretical massNumber of molelcules
Total (without water)22,4642
Polymers22,4642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-24 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.030, 107.030, 207.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11C-123-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROALAAA15 - 3327 - 45
21PROALABB15 - 3327 - 45
31PROALACC15 - 3327 - 45
41PROALADD15 - 3327 - 45
51PROALAEE15 - 3327 - 45
61PROALAFF15 - 3327 - 45
72GLUARGAA42 - 7854 - 90
82GLUARGBB42 - 7854 - 90
92GLUARGCC42 - 7854 - 90
102GLUARGDD42 - 7854 - 90
112GLUARGEE42 - 7854 - 90
122GLUARGFF42 - 7854 - 90

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Components

#1: Protein
exodeoxyribonuclease VII small subunit / Exonuclease VII


Mass: 11232.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / Gene: NP_881400.1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7W7Q2, UniProt: Q7VV85*PLUS, exodeoxyribonuclease VII
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 66.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 2.0M (NH4)2SO4, 2.0% PEG-400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.110.979694
SYNCHROTRONALS 8.3.120.979694,0.979811,1.020035
DetectorType: ADSC / Detector: CCD / Date: Sep 18, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796941
20.9798111
31.0200351
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
MOSFLMdata reduction
SCALA5.0)data scaling
SHELXmodel building
autoSHARPphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1388 4.9 %RANDOM
Rwork0.20268 ---
obs0.20473 26875 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.774 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.66 Å20 Å2
2--1.31 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 0 133 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223160
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0154288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9465409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72824.676139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04515539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0551531
X-RAY DIFFRACTIONr_chiral_restr0.0870.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022369
X-RAY DIFFRACTIONr_nbd_refined0.2160.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.28
X-RAY DIFFRACTIONr_mcbond_it2.90332146
X-RAY DIFFRACTIONr_mcangle_it3.85253322
X-RAY DIFFRACTIONr_scbond_it7.92581098
X-RAY DIFFRACTIONr_scangle_it11.23211966
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22242
Refine LS restraints NCS

Ens-ID: 1 / Number: 401 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.455
2Bloose positional0.555
3Cloose positional0.345
4Dloose positional0.375
5Eloose positional0.485
6Floose positional0.475
1Aloose thermal8.0910
2Bloose thermal6.0410
3Cloose thermal9.2310
4Dloose thermal6.9810
5Eloose thermal6.1210
6Floose thermal12.0410
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 84 4.1 %
Rwork0.228 1965 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1335-1.9324-1.42951.96031.27610.85460.03770.12450.2039-0.08820.0551-0.0489-0.12660.0867-0.0928-0.01790.01980.0005-0.05110.0014-0.011919.49966.60759.461
21.0636-1.5414-0.89683.55741.84411.0410.08150.08390.1184-0.04040.0259-0.1689-0.11720.07-0.1074-0.00210.01360.0503-0.04450.0011-0.029326.69761.07144.509
30.5205-0.8999-0.6533.40640.86480.857-0.0213-0.0404-0.01950.25270.035-0.246-0.1636-0.0017-0.0137-0.02830.0492-0.03740.0079-0.0212-0.029323.81463.27277.542
43.2018-2.4325-2.49693.56093.04822.72090.0373-0.27360.1910.16430.0709-0.1791-0.05230.2339-0.10810.09660.0856-0.06420.0137-0.0463-0.117219.27672.35892.687
54.1677-1.2474-1.6430.65271.29613.96960.07160.45260.3405-0.2571-0.149-0.0511-0.1760.27290.07750.09860.09690.03020.03460.0936-0.07224.54363.04324.784
65.3613-2.2374-5.48343.31044.24977.3671-0.31370.1301-0.46940.04280.1215-0.0721-0.16650.26750.19220.08070.10770.07020.17390.1051-0.090533.88357.4079.763
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 8025 - 92
22BB10 - 8622 - 98
33CC9 - 7921 - 91
44DD13 - 8425 - 96
55EE13 - 7925 - 91
66FF13 - 7925 - 91

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