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- PDB-1rmf: STRUCTURES OF A MONOCLONAL ANTI-ICAM-1 ANTIBODY R6.5 FRAGMENT AT ... -

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Basic information

Entry
Database: PDB / ID: 1rmf
TitleSTRUCTURES OF A MONOCLONAL ANTI-ICAM-1 ANTIBODY R6.5 FRAGMENT AT 2.8 ANGSTROMS RESOLUTION
Components
  • IGG2A-KAPPA R6.5 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA R6.5 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsJedrzejas, M.J. / Luo, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of a monoclonal anti-ICAM-1 antibody R6.5 Fab fragment at 2.8 A resolution.
Authors: Jedrzejas, M.J. / Miglietta, J. / Griffin, J.A. / Luo, M.
History
DepositionDec 16, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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: IGG2A-KAPPA R6.5 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA R6.5 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,1842
Polymers47,1842
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-31 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.360, 137.760, 91.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 100 / 3: CIS PROLINE - PRO L 146 / 4: CIS PROLINE - PRO H 9
5: ALA H 131 - PRO H 132 OMEGA = 220.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: CIS PROLINE - PRO H 153 / 7: CIS PROLINE - PRO H 155
8: TRP H 194 - PRO H 195 OMEGA = 51.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Antibody IGG2A-KAPPA R6.5 FAB (LIGHT CHAIN)


Mass: 24068.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: S16112
#2: Antibody IGG2A-KAPPA R6.5 FAB (HEAVY CHAIN)


Mass: 23114.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 2852989
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal grow
*PLUS
pH: 8.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mMborate1reservoir
28 %PEG1drop

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Data collection

ReflectionNum. obs: 12598 / % possible obs: 84.1 % / Observed criterion σ(I): 2
Reflection
*PLUS
Observed criterion σ(I): 25.2 / Num. measured all: 32642 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6.5 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.188 -
obs0.188 10606
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 0 117 4208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.2
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
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 28.2

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