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- PDB-7ads: Orf virus Apoptosis inhibitor ORFV125 -

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Basic information

Entry
Database: PDB / ID: 7ads
TitleOrf virus Apoptosis inhibitor ORFV125
ComponentsApoptosis inhibitor
KeywordsAPOPTOSIS / Orf virus / Bcl-2 / ITC
Function / homologymembrane / metal ion binding / Apoptosis inhibitor
Function and homology information
Biological speciesOrf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22032046456 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
CitationJournal: Biochem.J. / Year: 2020
Title: Crystal structures of ORFV125 provide insight into orf virus-mediated inhibition of apoptosis.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionSep 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 1, 2024Group: 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: Apoptosis inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,87819
Polymers16,1601
Non-polymers71818
Water48627
1
A: Apoptosis inhibitor
hetero molecules

A: Apoptosis inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,75638
Polymers32,3212
Non-polymers1,43536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area8820 Å2
ΔGint-147 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.613, 106.613, 60.589
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-310-

NA

21A-318-

MG

31A-421-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Apoptosis inhibitor


Mass: 16160.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus / Gene: ORFV125, ORF125 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0R8HV90

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Non-polymers , 5 types, 45 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.93 % / Description: Thick diamond shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium citrate tribasic dehydrate 0.02M magnesium chloride 0.1M Bis tris propane 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.22→50.66 Å / Num. obs: 10487 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 54.1483471542 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2
Reflection shellResolution: 2.22→2.29 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 929 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ORFV_Bax

Resolution: 2.22032046456→50.6556463757 Å / SU ML: 0.254351495517 / Cross valid method: FREE R-VALUE / σ(F): 1.34373156719 / Phase error: 35.3922298752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260389441726 547 5.22395186706 %
Rwork0.243985831367 9924 -
obs0.244911480668 10471 99.8474301516 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.22032046456→50.6556463757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 39 27 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002987174105971079
X-RAY DIFFRACTIONf_angle_d0.540382658031450
X-RAY DIFFRACTIONf_chiral_restr0.0338872290032166
X-RAY DIFFRACTIONf_plane_restr0.00393533657359190
X-RAY DIFFRACTIONf_dihedral_angle_d21.7635330194661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22032046456-2.44380.3795227554891270.3204595679442415X-RAY DIFFRACTION99.6862745098
2.4438-2.79730.3242362923971360.2788129257312429X-RAY DIFFRACTION99.7278382582
2.7973-3.52420.313545501131220.2665035342982477X-RAY DIFFRACTION100
3.5242-3.52420.22650558011620.2225663859542603X-RAY DIFFRACTION99.9638467101
Refinement TLS params.Method: refined / Origin x: 9.40899266467 Å / Origin y: 41.0463426487 Å / Origin z: -1.1337065775 Å
111213212223313233
T0.301678761017 Å20.0108171956556 Å20.0547187548281 Å2-0.551426490284 Å20.0503803628688 Å2--0.415049127359 Å2
L3.70502464954 °20.0241551711648 °2-0.418824587851 °2-1.95764026035 °20.493708386598 °2--1.46269583962 °2
S0.0516673517366 Å °-0.113429748602 Å °-0.114620044656 Å °0.0191326214981 Å °-0.0850442889679 Å °0.0816008080312 Å °0.103426894527 Å °-0.299880629285 Å °-0.0137227483602 Å °
Refinement TLS groupSelection details: all

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