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- PDB-2g75: Crystal Structure of anti-SARS m396 Antibody -

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Basic information

Entry
Database: PDB / ID: 2g75
TitleCrystal Structure of anti-SARS m396 Antibody
Components
  • IGG Heavy Chain
  • IGG Light Chain
KeywordsIMMUNE SYSTEM / SARS / S protein / antibody / epitopes / vaccines / inhibitors
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPrabakaran, P. / Gan, J.H. / Feng, Y. / Zhu, Z.Y. / Xiao, X.D. / Ji, X. / Dimitrov, D.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody.
Authors: Prabakaran, P. / Gan, J. / Feng, Y. / Zhu, Z. / Choudhry, V. / Xiao, X. / Ji, X. / Dimitrov, D.S.
History
DepositionFeb 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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: IGG Heavy Chain
B: IGG Light Chain
C: IGG Heavy Chain
D: IGG Light Chain


Theoretical massNumber of molelcules
Total (without water)97,5744
Polymers97,5744
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: IGG Heavy Chain
B: IGG Light Chain


Theoretical massNumber of molelcules
Total (without water)48,7872
Polymers48,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-23 kcal/mol
Surface area19850 Å2
MethodPISA
3
C: IGG Heavy Chain
D: IGG Light Chain


Theoretical massNumber of molelcules
Total (without water)48,7872
Polymers48,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-21 kcal/mol
Surface area19770 Å2
MethodPISA
4
A: IGG Heavy Chain
B: IGG Light Chain

C: IGG Heavy Chain
D: IGG Light Chain


Theoretical massNumber of molelcules
Total (without water)97,5744
Polymers97,5744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)69.066, 69.066, 166.656
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody IGG Heavy Chain


Mass: 25979.938 Da / Num. of mol.: 2 / Fragment: Fab m396, Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: recombinant antibody Fab / Plasmid: pDZ1.0 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#2: Antibody IGG Light Chain


Mass: 22807.094 Da / Num. of mol.: 2 / Fragment: Fab m396, Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: recombinant antibody Fab / Plasmid: pDZ1.0 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Fragment: Water / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% v/v Glycerol, 16% v/v Ethylene Glycol, 20% w/v PEG 6000, and 100 mM NaCl in 30 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 14, 2005 / Details: Mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→29.91 Å / Num. all: 34411 / Num. obs: 34411 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1950 / % possible all: 42.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DD8

2dd8


Resolution: 2.28→29.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 334072.45 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1679 4.9 %RANDOM
Rwork0.221 ---
all0.224 34030 --
obs0.221 34030 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0599 Å2 / ksol: 0.344674 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.78 Å21.44 Å20 Å2
2---8.78 Å20 Å2
3---17.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-30 Å
Luzzati sigma a0.47 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.28→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 0 176 6560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.631.5
X-RAY DIFFRACTIONc_mcangle_it5.332
X-RAY DIFFRACTIONc_scbond_it5.842
X-RAY DIFFRACTIONc_scangle_it7.462.5
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 152 5 %
Rwork0.352 2912 -
obs--45.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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