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- PDB-1sbs: CRYSTAL STRUCTURE OF AN ANTI-HCG FAB -

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Basic information

Entry
Database: PDB / ID: 1sbs
TitleCRYSTAL STRUCTURE OF AN ANTI-HCG FAB
Components(MONOCLONAL ANTIBODY 3A2) x 2
KeywordsMONOCLONAL ANTIBODY / FAB-FRAGMENT / REPRODUCTION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFotinou, C. / Beauchamp, J. / Emsley, P. / Dehaan, A. / Schielen, W.J.G. / Bos, E. / Isaacs, N.W.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structure of an Fab fragment against a C-terminal peptide of hCG at 2.0 A resolution.
Authors: Fotinou, C. / Beauchamp, J. / Emsley, P. / deHaan, A. / Schielen, W.J. / Bos, E. / Isaacs, N.W.
History
DepositionApr 8, 1998Processing site: BNL
Revision 1.0Apr 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: MONOCLONAL ANTIBODY 3A2
L: MONOCLONAL ANTIBODY 3A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6553
Polymers48,5592
Non-polymers961
Water17,006944
1
H: MONOCLONAL ANTIBODY 3A2
L: MONOCLONAL ANTIBODY 3A2
hetero molecules

H: MONOCLONAL ANTIBODY 3A2
L: MONOCLONAL ANTIBODY 3A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3106
Polymers97,1184
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 74.800, 198.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody MONOCLONAL ANTIBODY 3A2


Mass: 24131.965 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: HYBRIDOMA CELL / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1042226
#2: Antibody MONOCLONAL ANTIBODY 3A2


Mass: 24426.975 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: HYBRIDOMA CELL / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1407830
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / 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: 3.7 Å3/Da / Density % sol: 66 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 Mammonium sulfate1drop
32 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 43925 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.8 / % possible all: 93
Reflection
*PLUS
Num. measured all: 174451
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGF

1igf


Resolution: 2→20 Å / Cross valid method: THROUGHOUT
Details: POSITIONAL REFINEMENT WITH X-PLOR. R_CRYS=36%, R_FREE=41%. UNRESTRAINED B-FACTOR REFINEMENT USING SFALL. R_CRYS=23.8%, R_FREE=33.8%. THE REFINEMENT CONTINUED USING ONLY REFMAC. R_CRYS=18.2%, ...Details: POSITIONAL REFINEMENT WITH X-PLOR. R_CRYS=36%, R_FREE=41%. UNRESTRAINED B-FACTOR REFINEMENT USING SFALL. R_CRYS=23.8%, R_FREE=33.8%. THE REFINEMENT CONTINUED USING ONLY REFMAC. R_CRYS=18.2%, R_FREE=24.1% THE SEARCHING FOR WATER POSITIONS WAS PERFORMED USING ARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1354 3.08 %RANDOM
Rwork0.18 ---
obs0.18 43856 99 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 5 944 4360
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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