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- PDB-3w9d: Structure of Human Monoclonal Antibody E317 Fab -

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Basic information

Entry
Database: PDB / ID: 3w9d
TitleStructure of Human Monoclonal Antibody E317 Fab
Components
  • Antibody Fab heavy chain
  • Antibody Fab light chain
KeywordsIMMUNE SYSTEM / IgG fold / HSV gD
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLee, C.C. / Lin, L.L. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis for the antibody neutralization of herpes simplex virus
Authors: Lee, C.C. / Lin, L.L. / Chan, W.E. / Ko, T.P. / Lai, J.S. / Wang, A.H.J.
History
DepositionApr 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 28, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Antibody Fab heavy chain
B: Antibody Fab light chain
C: Antibody Fab heavy chain
D: Antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)93,5044
Polymers93,5044
Non-polymers00
Water9,998555
1
A: Antibody Fab heavy chain
B: Antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,7522
Polymers46,7522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: Antibody Fab heavy chain
D: Antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,7522
Polymers46,7522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.781, 90.722, 128.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Antibody Fab heavy chain


Mass: 23618.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab light chain


Mass: 23133.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 25%(w/v) PEG 4000, 10mM calcium chloride dihydrate, 100mM sodium citrate tribasic dihydrate, pH 5.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. all: 41992 / Num. obs: 40644 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→23 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.477 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25929 2054 5.1 %random
Rwork0.19045 ---
obs0.19396 38517 96.07 %-
all-38950 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2---1.6 Å2-0 Å2
3---4 Å2
Refinement stepCycle: LAST / Resolution: 2.32→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 0 555 6950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026542
X-RAY DIFFRACTIONr_bond_other_d0.0010.026076
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9588907
X-RAY DIFFRACTIONr_angle_other_deg0.8163.00214046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9885837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09724.286245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.141151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791528
X-RAY DIFFRACTIONr_chiral_restr0.0890.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3343.123372
X-RAY DIFFRACTIONr_mcbond_other2.3343.1193371
X-RAY DIFFRACTIONr_mcangle_it3.7974.664201
X-RAY DIFFRACTIONr_scbond_it2.4843.3213170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.316→2.376 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 154 -
Rwork0.249 2707 -
obs--93.8 %

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