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- PDB-1bvl: HUMANIZED ANTI-LYSOZYME FV -

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Basic information

Entry
Database: PDB / ID: 1bvl
TitleHUMANIZED ANTI-LYSOZYME FV
Components(HULYS11) x 2
KeywordsHUMANIZED ANTIBODY / FV / ANTI-LYSOZYME
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsHolmes, M.A. / Foote, J.
Citation
Journal: J.Immunol. / Year: 1997
Title: Structural consequences of humanizing an antibody.
Authors: Holmes, M.A. / Foote, J.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Antibody Framework Residues Affecting the Conformation of the Hypervariable Loops
Authors: Foote, J. / Winter, G.
History
DepositionSep 16, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: 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
A: HULYS11
B: HULYS11
C: HULYS11
D: HULYS11


Theoretical massNumber of molelcules
Total (without water)49,6694
Polymers49,6694
Non-polymers00
Water00
1
A: HULYS11
B: HULYS11


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,8352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area10160 Å2
MethodPISA
2
C: HULYS11
D: HULYS11


Theoretical massNumber of molelcules
Total (without water)24,8352
Polymers24,8352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.000, 143.000, 72.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.839814, -0.234724, -0.489508), (-0.335832, 0.933082, 0.128741), (0.426533, 0.272511, -0.862443)
Vector: 143.78841, 50.8787, 6.2959)

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Components

#1: Antibody HULYS11


Mass: 12872.358 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Genus: Homo, Mus / Species: , / Strain: , / Description: DESIGNED MOLECULE / Plasmid: LACZ/PELB / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / References: PIR: S21681
#2: Antibody HULYS11


Mass: 11962.320 Da / Num. of mol.: 2 / Fragment: FV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Genus: Homo, Mus / Species: , / Strain: , / Description: DESIGNED MOLECULE / Plasmid: LACZ/PELB / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / References: PIR: S21680
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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.7-0.8 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: R-AXIS IIC
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.87 Å / Num. obs: 16782 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.5
Reflection shellResolution: 2.87→3 Å / Mean I/σ(I) obs: 2.61 / % possible all: 83.3
Reflection
*PLUS
Num. measured all: 75768
Reflection shell
*PLUS
% possible obs: 83.3 %

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Processing

Software
NameVersionClassification
R-AXISdata collection
R-AXISdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: 1 B-FACTOR PER RESIDUE / σ(F): 2
Details: SOME ROUNDS OF TNT REFINEMENT WERE INTERSPERSED WITH THE X-PLOR REFINEMENT.
RfactorNum. reflection% reflection
Rwork0.22 --
obs0.22 16255 93.7 %
Displacement parametersBiso mean: 23.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.87→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 0 0 3488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
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
LS refinement shellResolution: 2.87→3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.293 1779 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.59 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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