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- PDB-3c08: Crystal structure the Fab fragment of matuzumab/EMD72000 (Fab72000) -

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Basic information

Entry
Database: PDB / ID: 3c08
TitleCrystal structure the Fab fragment of matuzumab/EMD72000 (Fab72000)
Components
  • Matuzumab Fab Heavy chain
  • Matuzumab Fab Light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ANTITUMOR / DRUG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsFerguson, K.M. / Schmiedel, J. / Knoechel, T.
CitationJournal: Cancer Cell / Year: 2008
Title: Matuzumab binding to EGFR prevents the conformational rearrangement required for dimerization.
Authors: Schmiedel, J. / Blaukat, A. / Li, S. / Knochel, T. / Ferguson, K.M.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2019Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_genus ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_genus / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_cell_line / _software.version
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Matuzumab Fab Light chain
H: Matuzumab Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5164
Polymers47,3232
Non-polymers1922
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-44 kcal/mol
Surface area18360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.821, 61.377, 102.675
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 Matuzumab Fab Light chain


Mass: 23235.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human/mouse chimeric derivative of mouse monoclonal antibody 425
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Cell line (production host): MYELOMA / Production host: Mus musculus (house mouse)
#2: Antibody Matuzumab Fab Heavy chain


Mass: 24087.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human/mouse chimeric derivative of mouse monoclonal antibody 425
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Cell line (production host): MYELOMA / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.79 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.15→52.7 Å / Num. all: 20191 / Num. obs: 20191 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Χ2: 1.361 / Net I/σ(I): 7.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.618 / Num. unique all: 1971 / Rsym value: 0.417 / Χ2: 0.931 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.72 Å
Translation2.5 Å49.72 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 20127
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.63-10025.80.18504
6.02-7.6330.30.72502
5.22-6.0222.40.814508
4.72-5.22210.853504
4.38-4.7219.40.897504
4.1-4.3819.20.882543
3.86-4.118.70.895566
3.67-3.8621.80.866598
3.5-3.6720.90.877632
3.35-3.522.50.855646
3.22-3.3520.60.866672
3.1-3.2224.30.852714
3-3.124.80.847717
2.9-328.30.823763
2.82-2.925.30.83764
2.74-2.82280.814801
2.66-2.7428.70.818812
2.6-2.6628.20.827831
2.53-2.627.60.804861
2.48-2.5327.50.811870
2.42-2.4829.40.797897
2.37-2.4227.40.816907
2.32-2.3732.20.791928
2.28-2.3229.70.8943
2.24-2.2829.90.795991
2.2-2.2436.80.739957
2.15-2.233.60.7321192

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DM6phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id 1L7I

1l7i


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.362 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1029 5.1 %RANDOM
Rwork0.224 ---
all0.226 20127 --
obs0.226 20127 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.434 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--1.35 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 10 99 3206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213233
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9524430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.2775423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50224.425113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.367157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022425
X-RAY DIFFRACTIONr_nbd_refined0.2220.21264
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.29
X-RAY DIFFRACTIONr_mcbond_it0.8321.52124
X-RAY DIFFRACTIONr_mcangle_it1.29723397
X-RAY DIFFRACTIONr_scbond_it1.1931109
X-RAY DIFFRACTIONr_scangle_it1.8854.51033
LS refinement shellResolution: 2.145→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 66 -
Rwork0.243 1275 -
all-1341 -
obs--90.85 %

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