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- PDB-5wtt: Structure of the 093G9 Fab in complex with the epitope peptide -

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Basic information

Entry
Database: PDB / ID: 5wtt
TitleStructure of the 093G9 Fab in complex with the epitope peptide
Components
  • Epitope peptide of Cyr61
  • Heavy chain of 093G9 Fab
  • Light chain of 093G9 Fab
KeywordsPROTEIN BINDING / Cyr61 / epitope / rheumatoid arthritis / therapeutic antibody 093G9
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsZhong, C. / Hu, K. / Shen, J. / Ding, J.
CitationJournal: J. Mol. Recognit. / Year: 2017
Title: Molecular basis for the recognition of CCN1 by monoclonal antibody 093G9.
Authors: Zhong, C. / Huo, R. / Hu, K. / Shen, J. / Li, D. / Li, N. / Ding, J.
History
DepositionDec 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Heavy chain of 093G9 Fab
L: Light chain of 093G9 Fab
P: Epitope peptide of Cyr61
A: Heavy chain of 093G9 Fab
B: Light chain of 093G9 Fab
C: Epitope peptide of Cyr61


Theoretical massNumber of molelcules
Total (without water)107,1226
Polymers107,1226
Non-polymers00
Water43224
1
H: Heavy chain of 093G9 Fab
L: Light chain of 093G9 Fab
P: Epitope peptide of Cyr61


Theoretical massNumber of molelcules
Total (without water)53,5613
Polymers53,5613
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-27 kcal/mol
Surface area19880 Å2
MethodPISA
2
A: Heavy chain of 093G9 Fab
B: Light chain of 093G9 Fab
C: Epitope peptide of Cyr61


Theoretical massNumber of molelcules
Total (without water)53,5613
Polymers53,5613
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.883, 214.437, 50.045
Angle α, β, γ (deg.)90.00, 92.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Heavy chain of 093G9 Fab


Mass: 26205.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Light chain of 093G9 Fab


Mass: 26513.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Protein/peptide Epitope peptide of Cyr61


Mass: 841.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 6000, 8% MPD, pH7.9, 5% ethyle acetate / PH range: 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jan 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 23993 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data processing
PHENIXphasing
RefinementResolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 18.178 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.413
RfactorNum. reflection% reflectionSelection details
Rfree0.27406 1221 5.1 %RANDOM
Rwork0.22189 ---
obs0.22456 22713 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.083 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å2-6.1 Å2
2---4.93 Å20 Å2
3---3.24 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 0 24 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026956
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9489473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3385872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49224.244271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.209151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4951526
X-RAY DIFFRACTIONr_chiral_restr0.0730.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215160
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7565.3973509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.8318.0934374
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.225.5443447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.09627165
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 88 -
Rwork0.343 1702 -
obs--98.03 %

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