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- PDB-5w05: ANTI-TISSUE FACTOR ANTIBODY M59, A HUMANIZED VERSION OF 10H10 -

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Basic information

Entry
Database: PDB / ID: 5w05
TitleANTI-TISSUE FACTOR ANTIBODY M59, A HUMANIZED VERSION OF 10H10
Components
  • M59 FAB HEAVY CHAIN
  • M59 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T.J. / Gilliland, G.L.
CitationJournal: MAbs / Year: 2018
Title: Structural insights into humanization of anti-tissue factor antibody 10H10.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Raghunathan, G. / Martinez, C. / Fransson, J. / Edwards, W. / Connor, J. / Husovsky, M. / Beck, H. / Chi, E. / Fenton, S. / Zhou, H. / Almagro, J.C. / Gilliland, G.L.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: 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
L: M59 FAB LIGHT CHAIN
H: M59 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8073
Polymers48,7012
Non-polymers1061
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-20 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.380, 80.650, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody M59 FAB LIGHT CHAIN


Mass: 24189.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody M59 FAB HEAVY CHAIN


Mass: 24511.443 Da / Num. of mol.: 1 / Fragment: FD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES PH 6.5, 16% PEG 3350, 0.2 M SODIUM FORMATE
PH range: 6.5

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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 SATURN 944 / Detector: CCD / Date: Mar 5, 2010 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 45702 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 38
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 2034 / % possible all: 56.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMAC5.8.0135refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m7k

4m7k


Resolution: 1.64→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.879 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1360 3 %RANDOM
Rwork0.18698 ---
obs0.18751 44257 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.64→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 7 355 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9534681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31624.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.781510
X-RAY DIFFRACTIONr_chiral_restr0.070.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212561
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_it1.892.1071756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7694.7232192
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8152.4881686
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.955458
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: 1.641→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 57 -
Rwork0.225 1962 -
obs--56.4 %

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