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- PDB-6fbj: monoclonal antibody targeting Matrix metalloproteinase 7 -

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Basic information

Entry
Database: PDB / ID: 6fbj
Titlemonoclonal antibody targeting Matrix metalloproteinase 7
Components
  • Heavy Chain
  • Light chain
KeywordsMETAL BINDING PROTEIN / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDym, O.
Funding support Israel, 1items
OrganizationGrant numberCountry
FP7-H2020 Israel
CitationJournal: To Be Published
Title: Novel monoclonal antibody targeting Matrix metalloproteinase 7 shows therapeutic potential against pancreatic cancer
Authors: Mohan, V. / Gaffney, J. / Klepfish, M. / Akbareian, S. / Grunwald, B. / Akkari, L. / Solomonov, I. / Dym, O. / Eisenstein, M. / Joyce, J. / Kruger, A. / Edwards, D. / Sagi, I.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 17, 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: Heavy Chain
L: Light chain


Theoretical massNumber of molelcules
Total (without water)47,7292
Polymers47,7292
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.443, 88.443, 119.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11L-324-

HOH

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Components

#1: Antibody Heavy Chain


Mass: 24014.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: BALB/c / Production host: Mus musculus (house mouse) / Variant (production host): Hybridoma
#2: Antibody Light chain /


Mass: 23715.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: BALB/c / Production host: Mus musculus (house mouse) / Variant (production host): Hybridoma
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.75 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M CaCl2 0.05M HEPES pH=7 10% PEG 6000 0.005M Betaine HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24579 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 33
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.58 / Num. unique obs: 1203 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPU

2ipu


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.131 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.222 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24927 1256 5.1 %RANDOM
Rwork0.20691 ---
obs0.20899 23291 99.69 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 56.198 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 0 62 3288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023386
X-RAY DIFFRACTIONr_bond_other_d0.0020.023003
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9434605
X-RAY DIFFRACTIONr_angle_other_deg0.9683.0017012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01324.255141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9161515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02677
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_it1.0662.6141706
X-RAY DIFFRACTIONr_mcbond_other0.9892.5981702
X-RAY DIFFRACTIONr_mcangle_it1.7133.9062122
X-RAY DIFFRACTIONr_mcangle_other1.6523.8932121
X-RAY DIFFRACTIONr_scbond_it1.2732.7371680
X-RAY DIFFRACTIONr_scbond_other1.2732.7431681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1194.0652484
X-RAY DIFFRACTIONr_long_range_B_refined5.04829.8813537
X-RAY DIFFRACTIONr_long_range_B_other5.04829.9153537
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 89 -
Rwork0.222 1647 -
obs--96.12 %
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)
12.0877-0.3391-0.93542.41730.17062.51620.22320.1860.313-0.1177-0.2186-0.028-0.3857-0.0582-0.00460.1580.06630.01040.1614-0.0070.066-32.707-5.99112.538
21.9773-0.5188-0.6422.6386-0.07632.5330.20560.15230.3169-0.1403-0.1424-0.333-0.45340.3356-0.06320.16090.03610.01780.23460.00480.0832-21.132-14.7341.097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 221
2X-RAY DIFFRACTION2L2 - 216

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