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- PDB-3f12: Germline V-genes sculpt the binding site of a family of antibodie... -

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Basic information

Entry
Database: PDB / ID: 3f12
TitleGermline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus
Components
  • 8f9 Fab
  • M2J1 Fab
KeywordsIMMUNE SYSTEM / Human cytomegalovirus / antibody / germline / Immunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsThomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W.
CitationJournal: Embo J. / Year: 2008
Title: Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus.
Authors: Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W.
History
DepositionOct 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M2J1 Fab
B: 8f9 Fab
C: M2J1 Fab
D: 8f9 Fab


Theoretical massNumber of molelcules
Total (without water)99,1334
Polymers99,1334
Non-polymers00
Water00
1
A: M2J1 Fab
B: 8f9 Fab


Theoretical massNumber of molelcules
Total (without water)49,5662
Polymers49,5662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23.4 kcal/mol
Surface area18960 Å2
MethodPISA
2
C: M2J1 Fab
D: 8f9 Fab


Theoretical massNumber of molelcules
Total (without water)49,5662
Polymers49,5662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-24.3 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.860, 87.860, 241.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody M2J1 Fab


Mass: 23723.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Antibody 8f9 Fab


Mass: 25842.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6
Details: 2.6 M Ammonium sulfate, 2% PEG 400 in CAPS buffer, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 23047 / Num. obs: 23047 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.12
Reflection shellResolution: 2.95→3.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.84 / % possible all: 98.4

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EYO

3eyo


Resolution: 2.95→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.32 1130 Random
Rwork0.3 --
all0.3 23047 -
obs0.32 22586 -
Displacement parametersBiso mean: 40.8 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 0 0 6303
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0212
X-RAY DIFFRACTIONc_angle_deg2.06

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