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- PDB-1bvk: HUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1bvk
TitleHUMANIZED ANTI-LYSOZYME FV COMPLEXED WITH LYSOZYME
Components
  • (HULYS11) x 2
  • LYSOZYME
KeywordsCOMPLEX (HUMANIZED ANTIBODY/HYDROLASE) / HUMANIZED ANTIBODY / ANTIBODY COMPLEX / FV / ANTI-LYSOZYME / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) / COMPLEX (HUMANIZED ANTIBODY-HYDROLASE) complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHolmes, M.A. / Buss, T.N. / Foote, J.
Citation
Journal: J.Exp.Med. / Year: 1998
Title: Conformational correction mechanisms aiding antigen recognition by a humanized antibody.
Authors: Holmes, M.A. / Buss, T.N. / Foote, J.
#1: Journal: J.Immunol. / Year: 1997
Title: Structural Consequences of Humanizing an Antibody
Authors: Holmes, M.A. / Foote, J.
#2: 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 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: HULYS11
B: HULYS11
C: LYSOZYME
D: HULYS11
E: HULYS11
F: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)78,3326
Polymers78,3326
Non-polymers00
Water00
1
A: HULYS11
B: HULYS11
C: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)39,1663
Polymers39,1663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HULYS11
E: HULYS11
F: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)39,1663
Polymers39,1663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.700, 97.700, 174.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999987, 0.002639, 0.004298), (-0.005041, 0.550415, 0.834876), (-0.000163, -0.834887, 0.550422)
Vector: 20.1259, -21.3587, 177.75011)

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Components

#1: 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 (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: PIR: S21680
#2: 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 (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: PIR: S21681
#3: Protein LYSOZYME / MURAMIDASE


Mass: 14331.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Description: EGG WHITE / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P00698, lysozyme
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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
21.6-1.7 Mphosphate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: R-AXIS IIC
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 22379 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.452 / Rsym value: 0.452 / % possible all: 73.5
Reflection
*PLUS
Num. measured all: 120820
Reflection shell
*PLUS
% possible obs: 73.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HULYS STRUCTURE, AND LYSOZYME FROM PDB ENTRY 1VFB

1vfb


Resolution: 2.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: A FEW CYCLES OF TNT REFINEMENT WERE INTERSPERSED WITH THE X-PLOR CYCLES.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1895 10.1 %RANDOM
Rwork0.208 ---
obs0.208 18822 80.3 %-
Displacement parametersBiso mean: 31.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 0 0 5490
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it9.916
X-RAY DIFFRACTIONx_mcangle_it11.78
X-RAY DIFFRACTIONx_scbond_it9.918
X-RAY DIFFRACTIONx_scangle_it11.710
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.38 148 10.1 %
Rwork0.326 1317 -
obs--50.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Rfactor obs: 0.326

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