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- PDB-2gj2: Crystal Structure of VP9 from White Spot Syndrome Virus -

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Basic information

Entry
Database: PDB / ID: 2gj2
TitleCrystal Structure of VP9 from White Spot Syndrome Virus
Componentswsv230
KeywordsMETAL BINDING PROTEIN / FERREDOXIN FOLD
Function / homologyVP9 protein domain / White spot syndrome virus (WSSV), Orf116/126, N-terminal / VP9, N-terminal domain superfamily / VP9 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / : / ICP11/P9
Function and homology information
Biological speciesShrimp white spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsLiu, Y. / Wu, J.L. / Song, J.X. / Sivaraman, J. / Hew, C.L.
CitationJournal: J.Virol. / Year: 2006
Title: Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites
Authors: Liu, Y. / Wu, J.L. / Song, J.X. / Sivaraman, J. / Hew, C.L.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: wsv230
B: wsv230
C: wsv230
D: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,90212
Polymers38,0034
Non-polymers8998
Water2,252125
1
A: wsv230
D: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4516
Polymers19,0012
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-31 kcal/mol
Surface area9350 Å2
MethodPISA
2
B: wsv230
C: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4516
Polymers19,0012
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-32 kcal/mol
Surface area9240 Å2
MethodPISA
3
C: wsv230
hetero molecules

D: wsv230
hetero molecules

A: wsv230
B: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,90212
Polymers38,0034
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-58 kcal/mol
Surface area16040 Å2
MethodPISA
4
C: wsv230
hetero molecules

A: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4516
Polymers19,0012
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area1970 Å2
ΔGint-26 kcal/mol
Surface area8590 Å2
MethodPISA
5
D: wsv230
hetero molecules

B: wsv230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4516
Polymers19,0012
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1810 Å2
ΔGint-23 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.133, 78.205, 78.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
wsv230 / VP9


Mass: 9500.659 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shrimp white spot syndrome virus / Genus: Whispovirus / Species: White spot syndrome virus 1 / Gene: WSV230 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q91LD0
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 2M sodium acetate, 100mM MES, 25mM cadmium sulfate, 3% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 38474 / Num. obs: 38474 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.27→2.35 Å / % possible all: 78.4

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→45 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1812 -RANDOM
Rwork0.225 ---
all-43491 --
obs-34301 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.35→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 8 125 2585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7

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