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- PDB-4x80: Crystal Structure of murine 7B4 Fab monoclonal antibody against A... -

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Basic information

Entry
Database: PDB / ID: 4x80
TitleCrystal Structure of murine 7B4 Fab monoclonal antibody against ADAMTS5
Components
  • IgG1 7B4 FAB Heavy chain
  • IgG1 7B4 FAB Light Chain
KeywordsIMMUNE SYSTEM / monoclonal
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLarkin, J. / Lohr, T.A. / Elefante, L. / Shearin, J. / Matico, R. / Su, J.-L. / Xue, Y. / Liu, F. / Genell, C. / Miller, R.E. ...Larkin, J. / Lohr, T.A. / Elefante, L. / Shearin, J. / Matico, R. / Su, J.-L. / Xue, Y. / Liu, F. / Genell, C. / Miller, R.E. / Tran, P.B. / Malfait, A.-M. / Maier, C.C. / Matheny, C.J.
CitationJournal: Osteoarthr. Cartil. / Year: 2015
Title: Translational development of an ADAMTS-5 antibody for osteoarthritis disease modification.
Authors: Larkin, J. / Lohr, T.A. / Elefante, L. / Shearin, J. / Matico, R. / Su, J.L. / Xue, Y. / Liu, F. / Genell, C. / Miller, R.E. / Tran, P.B. / Malfait, A.M. / Maier, C.C. / Matheny, C.J.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Data collection
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG1 7B4 FAB Light Chain
H: IgG1 7B4 FAB Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6942
Polymers47,6942
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-23 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.426, 78.007, 80.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IgG1 7B4 FAB Light Chain


Mass: 23502.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: hybridoma / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody IgG1 7B4 FAB Heavy chain


Mass: 24190.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% Peg 3350, 0.2 M Ammonium fluoride, 0.1 M Hepes pH 7.5
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 13771 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.111 / Χ2: 1.12 / Net I/av σ(I): 14.516 / Net I/σ(I): 7.7 / Num. measured all: 74977
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.695.20.45213211.07897.9
2.69-2.85.50.38913481.06299
2.8-2.935.60.30613411.12799.1
2.93-3.085.60.24113441.18499.3
3.08-3.285.50.17913721.17199
3.28-3.535.60.12713681.11599.6
3.53-3.885.50.09313731.10599.4
3.88-4.445.50.0713901.11799.7
4.44-5.595.40.05614091.1299.7
5.59-305.10.04215051.11499.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.21 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2734 / WRfactor Rwork: 0.2059 / FOM work R set: 0.7591 / SU B: 35.677 / SU ML: 0.342 / SU R Cruickshank DPI: 0.293 / SU Rfree: 0.4009 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 770 6 %RANDOM
Rwork0.2184 12140 --
obs0.222 12140 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.61 Å2 / Biso mean: 36.365 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å2-0 Å2
2---1.33 Å20 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 2.6→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 27 3325
Biso mean---24.34 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023383
X-RAY DIFFRACTIONr_bond_other_d0.0010.023148
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.9434610
X-RAY DIFFRACTIONr_angle_other_deg0.65337117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37423.969131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44715522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5841514
X-RAY DIFFRACTIONr_chiral_restr0.0560.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_mcbond_it0.9213.1991740
X-RAY DIFFRACTIONr_mcbond_other0.9213.1991740
X-RAY DIFFRACTIONr_mcangle_it1.6944.792170
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 60 -
Rwork0.32 754 -
all-814 -
obs--82.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6244-0.55350.01360.7358-0.03220.18910.02960.029-0.0182-0.0886-0.05030.0727-0.01680.03860.02070.020.003-0.01970.0108-0.00210.03142.145-1.4103-6.6919
20.5397-0.54620.16510.6824-0.18330.07990.0055-0.0803-0.03-0.01370.04070.05070.0122-0.0024-0.04620.0175-0.006-0.01070.0461-0.01570.04226.2407-2.122411.3689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 213
2X-RAY DIFFRACTION2H1 - 224

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