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- PDB-4x8j: Crystal Structure of murine 12F4 Fab monoclonal antibody against ... -

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Basic information

Entry
Database: PDB / ID: 4x8j
TitleCrystal Structure of murine 12F4 Fab monoclonal antibody against ADAMTS5
Components
  • 12F4 FAB Heavy chain
  • 12F4 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: 2.35 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 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 12F4 FAB Light chain
H: 12F4 FAB Heavy chain
B: 12F4 FAB Light chain
A: 12F4 FAB Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5438
Polymers94,5834
Non-polymers9604
Water5,747319
1
L: 12F4 FAB Light chain
H: 12F4 FAB Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2516
Polymers47,2922
Non-polymers9604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-97 kcal/mol
Surface area19960 Å2
MethodPISA
2
B: 12F4 FAB Light chain
A: 12F4 FAB Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,2922
Polymers47,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.080, 149.080, 116.774
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-325-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 214
2010B1 - 214
1020H1 - 214
2020A1 - 214

NCS ensembles :
ID
1
2

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Components

#1: Antibody 12F4 FAB Light chain


Mass: 23771.275 Da / Num. of mol.: 2
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)
#2: Antibody 12F4 FAB Heavy chain


Mass: 23520.389 Da / Num. of mol.: 2
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2M Zinc acetate, 20% PEG3350

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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: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 55390 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.091 / Χ2: 1.04 / Net I/av σ(I): 27.773 / Net I/σ(I): 10.7 / Num. measured all: 762232
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
2.35-2.4313.90.58254600.955
2.43-2.5313.90.45954421.005
2.53-2.6513.90.35654571.043
2.65-2.7913.90.26254841.081
2.79-2.9613.90.18354681.06
2.96-3.1913.90.12255051.057
3.19-3.5113.80.0955331.045
3.51-4.0213.80.08355561.052
4.02-5.0613.60.05456111.076
5.06-30130.04258741.021

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2407 / WRfactor Rwork: 0.2206 / FOM work R set: 0.8181 / SU B: 12.495 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2625 / SU Rfree: 0.1987 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2677 4.8 %RANDOM
Rwork0.2168 52650 --
obs0.2176 52650 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.79 Å2 / Biso mean: 48.587 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 58 319 6646
Biso mean--48.51 40.38 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.026516
X-RAY DIFFRACTIONr_bond_other_d0.0020.025858
X-RAY DIFFRACTIONr_angle_refined_deg0.9451.9428870
X-RAY DIFFRACTIONr_angle_other_deg0.735313557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3225830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17324.387253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70915986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161524
X-RAY DIFFRACTIONr_chiral_restr0.0590.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021454
X-RAY DIFFRACTIONr_mcbond_it0.6892.9133320
X-RAY DIFFRACTIONr_mcbond_other0.6892.9133319
X-RAY DIFFRACTIONr_mcangle_it1.2664.3654141
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L111410.1
12B111410.1
21H97910.09
22A97910.09
LS refinement shellResolution: 2.35→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 194 -
Rwork0.281 3745 -
all-3939 -
obs--97.4 %
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)
10.52180.62680.32651.44820.90820.6082-0.1520.0379-0.0117-0.24560.15710.0027-0.08150.0612-0.00510.3061-0.0927-0.01780.15590.03230.0076-30.24350.6081.911
20.73720.64151.13590.71211.4173.0474-0.01420.1594-0.13220.03040.1447-0.08520.23920.1685-0.13050.3013-0.0696-0.03550.1523-0.03410.0461-18.79537.8256.172
30.843-0.0429-0.40070.8222-0.85933.11990.1470.22070.1683-0.0450.15180.0885-0.3647-0.2999-0.29880.17990.01350.05120.13650.05620.0533-54.60823.293-8.387
40.8749-0.1714-1.04180.1075-0.2384.0930.44330.33160.3319-0.026-0.0446-0.0681-0.7771-0.573-0.39860.34530.17930.15610.23080.13980.1293-64.94233.6792.065
516.14483.177-15.91584.7567-11.576832.9548-0.5102-0.0507-0.5324-0.10640.0149-0.09620.5047-0.01210.49540.15950.1320.08190.12940.05720.2641-8.77558.25732.517
631.0551-4.19711.108435.922814.780418.83620.2476-0.12570.74580.2018-0.48980.3422-0.1218-0.01610.24220.1665-0.01450.05160.1865-0.05160.1414-16.09165.6731.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 214
2X-RAY DIFFRACTION2H1 - 218
3X-RAY DIFFRACTION3B1 - 214
4X-RAY DIFFRACTION4A1 - 215
5X-RAY DIFFRACTION5D1 - 6
6X-RAY DIFFRACTION6E1 - 6

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