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- PDB-4ouu: anti-MT1-MMP monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 4ouu
Titleanti-MT1-MMP monoclonal antibody
Components
  • anti_MT1-MMP Heavy chain
  • anti_MT1-MMP light chain
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Israel Structural Proteomics Center / ISPC / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUdi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Koziol, A. / Cuniasse, P. / Dive, V. / Arroyo, A.G. / Irit, S. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Structure / Year: 2015
Title: Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody.
Authors: Udi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Moreno, V. / Cuniasse, P. / Dive, V. / Arroyo, A.G. / Sagi, I.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti_MT1-MMP Heavy chain
B: anti_MT1-MMP Heavy chain
L: anti_MT1-MMP light chain
A: anti_MT1-MMP light chain


Theoretical massNumber of molelcules
Total (without water)98,2404
Polymers98,2404
Non-polymers00
Water00
1
H: anti_MT1-MMP Heavy chain
L: anti_MT1-MMP light chain


Theoretical massNumber of molelcules
Total (without water)49,1202
Polymers49,1202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-25 kcal/mol
Surface area18830 Å2
MethodPISA
2
B: anti_MT1-MMP Heavy chain
A: anti_MT1-MMP light chain


Theoretical massNumber of molelcules
Total (without water)49,1202
Polymers49,1202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-25 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.140, 52.6, 127.500
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21B
12L
22A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALHA2 - 2162 - 216
21VALVALVALVALBB2 - 2162 - 216
12ASPASPASNASNLC1 - 2171 - 217
22ASPASPASNASNAD1 - 2171 - 217

NCS ensembles :
ID
1
2

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Components

#1: Antibody anti_MT1-MMP Heavy chain


Mass: 24995.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody anti_MT1-MMP light chain


Mass: 24124.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Potassium Formate 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97628 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.6→64 Å / Num. all: 79143 / Num. obs: 26041 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.112 / Rsym value: 0.075
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.525 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→52.22 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.892 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25271 1314 5.1 %RANDOM
Rwork0.1965 ---
obs0.19933 24702 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 0 6276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026481
X-RAY DIFFRACTIONr_bond_other_d0.0040.025843
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9468868
X-RAY DIFFRACTIONr_angle_other_deg0.9413.00213409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71522.783212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71515930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0651528
X-RAY DIFFRACTIONr_chiral_restr0.0850.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217412
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021491
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H107750.05
12B107750.05
21L109320.09
22A109320.09
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 104 -
Rwork0.326 1812 -
obs--98.51 %

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