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- PDB-1fgv: X-RAY STRUCTURES OF FRAGMENTS FROM BINDING AND NONBINDING VERSION... -

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Basic information

Entry
Database: PDB / ID: 1fgv
TitleX-RAY STRUCTURES OF FRAGMENTS FROM BINDING AND NONBINDING VERSIONS OF A HUMANIZED ANTI-CD18 ANTIBODY: STRUCTURAL INDICATIONS OF THE KEY ROLE OF VH RESIDUES 59 TO 65
Components
  • H52 FV (HEAVY CHAIN)
  • H52 FV (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsEigenbrot, C. / Kessler, J.
CitationJournal: Proteins / Year: 1994
Title: X-ray structures of fragments from binding and nonbinding versions of a humanized anti-CD18 antibody: structural indications of the key role of VH residues 59 to 65.
Authors: Eigenbrot, C. / Gonzalez, T. / Mayeda, J. / Carter, P. / Werther, W. / Hotaling, T. / Fox, J. / Kessler, J.
History
DepositionNov 1, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Nov 20, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: H52 FV (LIGHT CHAIN)
H: H52 FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)25,5992
Polymers25,5992
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.200, 61.300, 51.800
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95
Components on special symmetry positions
IDModelComponents
11H-720-

HOH

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Components

#1: Antibody H52 FV (LIGHT CHAIN)


Mass: 11907.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: GenBank: 259596
#2: Antibody H52 FV (HEAVY CHAIN)


Mass: 13692.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoir
415 %(w/v)PEG34001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 15 Å / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.231

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 2
Details: TWO SIDE CHAIN CONFORMATIONS ARE GIVEN FOR RESIDUES CYS 23 AND CYS 88.
RfactorNum. reflection
Rwork0.18 -
obs0.18 13122
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 109 1848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.8
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. reflection obs: 13122 / σ(F): 2 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d2.8
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_deg1.6
X-RAY DIFFRACTIONx_mcbond_it1.81
X-RAY DIFFRACTIONx_scbond_it3.31.5
X-RAY DIFFRACTIONx_mcangle_it2.91.5
X-RAY DIFFRACTIONx_scangle_it4.82

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