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- PDB-1p35: CRYSTAL STRUCTURE OF BACULOVIRUS P35 -

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Basic information

Entry
Database: PDB / ID: 1p35
TitleCRYSTAL STRUCTURE OF BACULOVIRUS P35
ComponentsP35
KeywordsAPOPTOSIS / P35 / CELL DEATH / BACULOVIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host RNAi-mediated antiviral immune response / symbiont-mediated suppression of host apoptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cysteine-type endopeptidase inhibitor activity / negative regulation of apoptotic process
Similarity search - Function
Baculovirus p35 / Baculovirus p35 / Baculovirus p35, apoptosis preventing protein / Baculovirus p35 superfamily / Apoptosis preventing protein / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Early 35 kDa protein
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsFisher, A.J. / Delacruz, W.P. / Zoog, S.J. / Schneider, C.L. / Friesen, P.D.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of baculovirus P35: role of a novel reactive site loop in apoptotic caspase inhibition.
Authors: Fisher, A.J. / Cruz, W. / Zoog, S.J. / Schneider, C.L. / Friesen, P.D.
History
DepositionSep 18, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: P35
B: P35
C: P35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9129
Polymers104,4413
Non-polymers4716
Water4,810267
1
A: P35
C: P35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9416
Polymers69,6272
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P35
hetero molecules

B: P35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9416
Polymers69,6272
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)114.580, 130.110, 181.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein P35


Mass: 34813.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Genus: Nucleopolyhedrovirus / Plasmid: BACULOVIRUS / Production host: Escherichia coli (E. coli) / References: UniProt: P08160
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 62 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: or batch
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
21.5-2.0 M1reservoirNa+/K+PO4
3100 mM1reservoirNaCl
41 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 66995 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1
Reflection
*PLUS
Num. obs: 66997 / Num. measured all: 324073

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Processing

Software
NameVersionClassification
PHASESphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 3350183.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3398 5.1 %RANDOM
Rwork0.196 ---
obs0.196 66995 97.6 %-
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.16 Å20 Å20 Å2
2--1.91 Å20 Å2
3---7.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7244 0 12 267 7523
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.831.5
X-RAY DIFFRACTIONc_mcangle_it9.892
X-RAY DIFFRACTIONc_scbond_it11.342
X-RAY DIFFRACTIONc_scangle_it13.412.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 551 5.1 %
Rwork0.292 10165 -
obs--94.5 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 66997 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.04
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor obs: 0.292

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