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- PDB-5dr5: Crystal structure of the sclerostin-neutralizing Fab AbD09097 -

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Basic information

Entry
Database: PDB / ID: 5dr5
TitleCrystal structure of the sclerostin-neutralizing Fab AbD09097
Components
  • AbD09097 Fab heavy chain
  • AbD09097 Fab light chain
KeywordsIMMUNE SYSTEM / sclerostin-neutralizing / Fab / Wnt inhibitor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsMueller, T.D. / Boschert, V. / Weidauer, S.E. / Muth, E.M. / Knappik, A. / Frisch, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationDFG MU1095/5-1 Germany
European UnionTALOS, HEALTH-F2-2008-201099
CitationJournal: to be published
Title: Generation and Affinity Maturation of Neutralizing Anti-Sclerostin Antibodies
Authors: Boschert, V. / Frisch, C. / Back, J.W. / van Pee, K. / Weidauer, S.E. / Muth, E.-M. / Schmieder, P. / Beerbaum, M. / Knappik, A. / Timmerman, P. / Mueller, T.D.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: AbD09097 Fab heavy chain
L: AbD09097 Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,2462
Polymers50,2462
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.193, 78.495, 59.196
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody AbD09097 Fab heavy chain


Mass: 26727.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Fab heavy chain contains a C-terminal Myc- and hexahistidine extension preceded by thrombin peptidase recognition sequence to facilitate detection and purification
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#2: Antibody AbD09097 Fab light chain


Mass: 23517.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TGF1-
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG3350, 0.1M HEPES pH 7.5, 10mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 13, 2012 / Details: Rigaku VariMax HF
RadiationMonochromator: multilayer mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20.77 Å / Num. all: 35146 / Num. obs: 34389 / % possible obs: 97.9 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 10.5 / Num. measured all: 126958 / Scaling rejects: 953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.85-1.922.940.33.7826128031.073280.1
1.92-1.993.490.2963.91210334431.098699
1.99-2.083.660.2494.51287734931.0478100
2.08-2.193.670.2214.91298435021.03116100
2.19-2.333.710.25.41312835111.04105100
2.33-2.513.750.147.31333435320.9474100
2.51-2.763.790.09610.11326634770.938799.9
2.76-3.163.820.06414.11351035170.868299.9
3.16-3.983.840.0518.71368635370.8789100
3.98-20.773.810.03428.11380935740.8820499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å20.77 Å
Translation1.85 Å20.77 Å

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Processing

Software
NameVersionClassification
CrystalClear9.2SSIdata collection
CrystalClear9.2SSIdata reduction
CrystalClear9.2SSIdata scaling
PHASER2.5.5phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NH7

3nh7


Resolution: 1.85→20.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2371 / WRfactor Rwork: 0.1797 / FOM work R set: 0.7912 / SU B: 9.789 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1613 / SU Rfree: 0.1552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1721 5 %RANDOM
Rwork0.1884 ---
obs0.1913 32559 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK / Bsol: 250.008 Å2 / ksol: 0.77 e/Å3
Displacement parametersBiso max: 71.06 Å2 / Biso mean: 29.759 Å2 / Biso min: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-1.18 Å2
2---0.23 Å20 Å2
3----0.4 Å2
Refine analyzeLuzzati coordinate error free: 0.263 Å
Refinement stepCycle: final / Resolution: 1.85→20.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 288 3634
Biso mean---34.33 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023446
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9544693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5635437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14524.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04915549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5291516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212608
X-RAY DIFFRACTIONr_mcbond_it1.72.0541754
X-RAY DIFFRACTIONr_mcangle_it2.5173.0692189
X-RAY DIFFRACTIONr_scbond_it2.2912.1891692
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 88 -
Rwork0.361 1900 -
all-1988 -
obs--76.85 %
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)
11.3525-0.60260.84662.5996-0.22061.9231-0.0144-0.0316-0.02540.1257-0.00340.15790.1488-0.19560.01780.0371-0.03260.03880.0935-0.03510.06585.2199-1.62433.0406
21.49710.77260.78571.39970.65781.5611-0.26790.07890.1955-0.24160.05160.1132-0.3491-0.10330.21630.08940.0097-0.05460.0246-0.00410.037913.466919.11320.7982
30.94360.22050.97920.9953-0.01571.59650.0474-0.1595-0.0072-0.061-0.00170.06710.0599-0.1166-0.04570.0133-0.01770.00870.09280.01090.055924.11672.664832.1163
41.093-0.48860.83621.7198-0.54411.1181-0.043-0.02220.03490.06790.0085-0.1184-0.0384-0.02620.03450.01540.00050.01420.0108-0.00050.037837.36928.326827.5698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 115
2X-RAY DIFFRACTION2L1 - 109
3X-RAY DIFFRACTION3H116 - 224
4X-RAY DIFFRACTION4L110 - 215

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