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- PDB-1i3s: THE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULO... -

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Basic information

Entry
Database: PDB / ID: 1i3s
TitleTHE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE
ComponentsEARLY 35 KDA PROTEIN
KeywordsAPOPTOSIS / hairpin loop / helix-turn-helix / reactive site loop
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Early 35 kDa protein
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EARLY 35 KDA PROTEIN
B: EARLY 35 KDA PROTEIN
C: EARLY 35 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6936
Polymers104,2313
Non-polymers4633
Water97354
1
A: EARLY 35 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8982
Polymers34,7441
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EARLY 35 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8982
Polymers34,7441
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: EARLY 35 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8982
Polymers34,7441
Non-polymers1541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.608, 89.303, 136.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

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


Mass: 34743.512 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Genus: Nucleopolyhedrovirus / Gene: P35 / Plasmid: PET22B+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08160
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: 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, temperature 298K
Crystal
*PLUS
Density % sol: 44.8 %
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
71-8 %MPD1drop
8100-400 mM1reservoirNaCl
99-13 %PEG200001reservoir
10100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2000 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 26627 / Num. obs: 25271 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.26 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 450.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.334 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 183500 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I3P

1i3p


Resolution: 2.7→29.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1079019.62 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1222 4.8 %RANDOM
Rwork0.202 ---
all0.213 183500 --
obs0.202 25271 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.49 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--12.67 Å20 Å20 Å2
2--10.22 Å20 Å2
3---2.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 24 54 6781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
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
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 203 4.9 %
Rwork0.238 3939 -
obs--95.1 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.238

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