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- PDB-5usl: Structure of vaccinia virus D8 protein bound to human Fab vv304 -

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Basic information

Entry
Database: PDB / ID: 5usl
TitleStructure of vaccinia virus D8 protein bound to human Fab vv304
Components
  • Fab vv304 Heavy chain
  • Fab vv304 Light chain
  • IMV membrane protein
KeywordsVIRAL PROTEIN/Immune System / viral protein / antibody / Fab / Immune response / Ig fold / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


regulation of pH / carbonate dehydratase activity / carbon dioxide transport / virion membrane / zinc ion binding / membrane
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Roll ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cell surface-binding protein OPG105
Similarity search - Component
Biological speciesVaccinia virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsZajonc, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)HHSN272200900048C United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8.
Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, ...Authors: Matho, M.H. / Schlossman, A. / Gilchuk, I.M. / Miller, G. / Mikulski, Z. / Hupfer, M. / Wang, J. / Bitra, A. / Meng, X. / Xiang, Y. / Kaever, T. / Doukov, T. / Ley, K. / Crotty, S. / Peters, B. / Hsieh-Wilson, L.C. / Crowe, J.E. / Zajonc, D.M.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: IMV membrane protein
A: IMV membrane protein
H: Fab vv304 Heavy chain
L: Fab vv304 Light chain
B: Fab vv304 Heavy chain
C: Fab vv304 Light chain


Theoretical massNumber of molelcules
Total (without water)148,5826
Polymers148,5826
Non-polymers00
Water00
1
X: IMV membrane protein
H: Fab vv304 Heavy chain
L: Fab vv304 Light chain


Theoretical massNumber of molelcules
Total (without water)74,2913
Polymers74,2913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: IMV membrane protein
B: Fab vv304 Heavy chain
C: Fab vv304 Light chain


Theoretical massNumber of molelcules
Total (without water)74,2913
Polymers74,2913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.980, 117.980, 104.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein IMV membrane protein


Mass: 27965.414 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235
Source method: isolated from a genetically manipulated source
Details: CAH domain, residues 1-235 / Source: (gene. exp.) Vaccinia virus / Gene: VAC_DPP17_124, VACAC2_124, VACCL3_124 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1M1K6
#2: Antibody Fab vv304 Heavy chain


Mass: 23809.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody Fab vv304 Light chain


Mass: 22515.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 200 mM sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2014
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.9→47.81 Å / Num. obs: 30196 / % possible obs: 94.8 % / Redundancy: 3.2 % / Rpim(I) all: 0.0112 / Net I/σ(I): 6.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4480 / Rpim(I) all: 0.57 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E9O, 3LMJ

4e9o

3lmj


Resolution: 2.9→47.81 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.819 / SU B: 22.836 / SU ML: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.529
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2973 1537 5.1 %RANDOM
Rwork0.2468 ---
obs0.2493 28658 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.15 Å2 / Biso mean: 56.55 Å2 / Biso min: 36.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.9→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10022 0 0 0 10022
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01910278
X-RAY DIFFRACTIONr_bond_other_d0.0010.029452
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.9514014
X-RAY DIFFRACTIONr_angle_other_deg0.6483.00121819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28651283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82224.813428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.986151614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2221528
X-RAY DIFFRACTIONr_chiral_restr0.0520.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022310
LS refinement shellResolution: 2.901→2.976 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 112 -
Rwork0.345 2157 -
all-2269 -
obs--97.22 %

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