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- PDB-1ghf: ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1ghf
TitleANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT
Components(ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT) x 2
KeywordsANTIBODY FAB FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBan, N. / Day, J. / Wang, X. / Ferrone, S. / McPherson, A.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of an anti-anti-idiotype shows it to be self-complementary.
Authors: Ban, N. / Day, J. / Wang, X. / Ferrone, S. / McPherson, A.
History
DepositionNov 30, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT
H: ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)46,5392
Polymers46,5392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-23 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.400, 150.400, 43.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Antibody ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT


Mass: 23427.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody ANTI-ANTI-IDIOTYPE GH1002 FAB FRAGMENT


Mass: 23111.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
26 %(w/v)PEG33501drop
312 %PEG33501reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 13743 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 65132
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 92 %

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Processing

Software
NameVersionClassification
HOWARDdata collection
NIELSENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLOR3.1phasing
RefinementResolution: 2.7→30 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.21 -
obs0.21 12323
Displacement parametersBiso mean: 10.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 0 0 3273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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