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- PDB-1i3p: THE 3.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULO... -

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Basic information

Entry
Database: PDB / ID: 1i3p
TitleTHE 3.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE
ComponentsEARLY 35 KDA PROTEIN
KeywordsAPOPTOSIS / helix-turn-helix / reactive site loop / hairpin loop
Function / homology
Function and homology information


symbiont-mediated suppression of host RNAi-mediated antiviral immune response / : / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / : / 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
Early 35 kDa protein
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
Authorsdela Cruz, W.P. / Lemongello, D. / Friesen, P.D. / Fisher, A.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of baculovirus P35 reveals a novel conformational change in the reactive site loop after caspase cleavage.
Authors: dela Cruz, W.P. / Friesen, P.D. / Fisher, A.J.
#1: Journal: Embo J. / Year: 1999
Title: Crystal structure of baculovirus P35: role of a novel reactive site loop in apoptotic inhibition
Authors: Fisher, A.J. / dela Cruz, W.P. / Zoog, S.J. / Schneider, C.L. / Friesen, P.D.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EARLY 35 KDA PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,7121
Polymers34,7121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.806, 75.806, 120.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer

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Components

#1: Protein EARLY 35 KDA PROTEIN / / APOPTOSIS PREVENTING PROTEIN


Mass: 34712.434 Da / Num. of mol.: 1 / Mutation: V71P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Genus: NucleopolyhedrovirusAlphabaculovirus / Gene: P35 / Plasmid: PET22B+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08160

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 9-13% PEG 20,000, 100-400 mM NaCl, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Density % sol: 62.1 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1dropNaCl
21 mMEDTA1drop
31 mMdithiothreitol1drop
41 mM1dropNaN3
520 mMHEPES1drop
65-8 mg/mlprotein1drop
7100-400 mM1reservoirNaCl
89-13 %PEG200001reservoir
9100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1999 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. all: 80534 / Num. obs: 7577 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 10.63 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 470.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.395 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 80534

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P35

1p35


Resolution: 3.1→14.95 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 934677.25 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 346 4.6 %RANDOM
Rwork0.239 ---
all0.2562 80534 --
obs0.239 7530 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.08 Å2 / ksol: 0.239 e/Å3
Displacement parametersBiso mean: 75.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.42 Å
Luzzati d res low-15 Å
Luzzati sigma a0.36 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 3.1→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 0 0 2077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
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_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.48
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 62 4.9 %
Rwork0.314 1191 -
obs--99.7 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 75.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.48
LS refinement shell
*PLUS
Rfactor Rfree: 0.384 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.314

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