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- PDB-6b9j: Structure of vaccinia virus D8 protein bound to human Fab vv138 -

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Basic information

Entry
Database: PDB / ID: 6b9j
TitleStructure of vaccinia virus D8 protein bound to human Fab vv138
Components
  • Fab vv138 Heavy chain
  • Fab vv138 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


carbonate dehydratase activity / 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 / 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
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionNov 22, 2017ID: 5USI
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
H: Fab vv138 Heavy chain
L: Fab vv138 Light chain
Y: IMV membrane protein
A: Fab vv138 Heavy chain
B: Fab vv138 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,57015
Polymers149,2256
Non-polymers3459
Water86548
1
X: IMV membrane protein
H: Fab vv138 Heavy chain
L: Fab vv138 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8199
Polymers74,6123
Non-polymers2076
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: IMV membrane protein
A: Fab vv138 Heavy chain
B: Fab vv138 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7506
Polymers74,6123
Non-polymers1383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.282, 253.842, 73.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Y
12H
22A
13H
23A
14L
24B
15L
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111X2 - 236
2111Y2 - 236
1121H1 - 116
2121A1 - 116
1131H117 - 217
2131A117 - 217
1141L1 - 91
2141B1 - 91
1241L97 - 105
2241B97 - 105
1151L110 - 215
2151B110 - 215

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.005768, 0.999939, -0.009427), (0.999969, 0.005817, 0.005269), (0.005324, -0.009396, -0.999942)-0.16465, 0.06071, -18.57748

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Components

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Protein , 1 types, 2 molecules XY

#1: Protein IMV membrane protein


Mass: 27965.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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

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Antibody , 2 types, 4 molecules HALB

#2: Antibody Fab vv138 Heavy chain


Mass: 23209.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody Fab vv138 Light chain


Mass: 23436.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 3 types, 57 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 200mM sodium malonate

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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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.905→172.163 Å / Num. all: 48731 / Num. obs: 48731 / % possible obs: 99.4 % / Redundancy: 6.2 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.179 / Rsym value: 0.163 / Net I/av σ(I): 4.3 / Net I/σ(I): 8.3 / Num. measured all: 301272
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.9-3.066.41.4330.54545470890.6071.5591.4331.499.8
3.06-3.256.20.8360.94144766480.3610.9120.8362.399.7
3.25-3.4760.4591.73716262370.2030.5030.4593.899
3.47-3.756.40.2982.53783458780.1260.3240.298699.9
3.75-4.115.90.193.93160753630.0850.2090.198.398.7
4.11-4.596.30.1196.13094149040.0510.130.11912.899.6
4.59-5.36.20.097.72679443380.0390.0980.0915.499.6
5.3-6.56.20.0877.92283836960.0380.0950.08715.299.2
6.5-9.1960.0758.41724128960.0330.0820.07517.599.2
9.19-117.1415.90.04812.1995416820.0210.0530.04824.399

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E9O, 1RZ7

4e9o

1rz7


Resolution: 2.9→117.14 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.905 / SU B: 20.14 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.901 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 2466 5.1 %RANDOM
Rwork0.2412 ---
obs0.2426 46251 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.8 Å2 / Biso mean: 87.27 Å2 / Biso min: 13.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.9→117.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9917 0 19 48 9984
Biso mean--68.97 61.53 -
Num. residues----1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910186
X-RAY DIFFRACTIONr_bond_other_d0.0060.029177
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.94513888
X-RAY DIFFRACTIONr_angle_other_deg0.924321184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23751293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81624.82417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.876151539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2711523
X-RAY DIFFRACTIONr_chiral_restr0.0640.21581
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022291
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1X35642.67
2H16554.19
3H13028.64
4L13806.82
5L123614.25
LS refinement shellResolution: 2.905→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 192 -
Rwork0.383 3401 -
all-3593 -
obs--99.83 %

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