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- PDB-3utz: Endogenous-like inhibitory antibodies targeting activated metallo... -

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Basic information

Entry
Database: PDB / ID: 3utz
TitleEndogenous-like inhibitory antibodies targeting activated metalloproteinase motifs show therapeutic potential
Components
  • Metalloproteinase, heavy chain
  • Metalloproteinase, light chain
KeywordsIMMUNE SYSTEM / Structural Genomics / Israel Structural Proteomics Center / ISPC / Fab domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsSela-Passwell, N. / Kikkeri, R. / Dym, O. / Rozenberg, H. / Margalit, R. / Arad-Yellin, R. / Eisenstein, M. / Brenner, O. / Shoham, T. / Danon, T. ...Sela-Passwell, N. / Kikkeri, R. / Dym, O. / Rozenberg, H. / Margalit, R. / Arad-Yellin, R. / Eisenstein, M. / Brenner, O. / Shoham, T. / Danon, T. / Shanzer, A. / Sagi, I. / Israel Structural Proteomics Center (ISPC)
CitationJournal: NAT.MED. (N.Y.) / Year: 2012
Title: Antibodies targeting the catalytic zinc complex of activated matrix metalloproteinases show therapeutic potential.
Authors: Sela-Passwell, N. / Kikkeri, R. / Dym, O. / Rozenberg, H. / Margalit, R. / Arad-Yellin, R. / Eisenstein, M. / Brenner, O. / Shoham, T. / Danon, T. / Shanzer, A. / Sagi, I.
History
DepositionNov 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Oct 2, 2013Group: Source and taxonomy
Revision 1.3Mar 26, 2014Group: Database references
Revision 1.4Mar 15, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metalloproteinase, light chain
B: Metalloproteinase, heavy chain
D: Metalloproteinase, light chain
C: Metalloproteinase, heavy chain
E: Metalloproteinase, light chain
F: Metalloproteinase, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,45216
Polymers144,4926
Non-polymers96110
Water905
1
A: Metalloproteinase, light chain
B: Metalloproteinase, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6447
Polymers48,1642
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-66 kcal/mol
Surface area18430 Å2
MethodPISA
2
D: Metalloproteinase, light chain
C: Metalloproteinase, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4525
Polymers48,1642
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-55 kcal/mol
Surface area18320 Å2
MethodPISA
3
E: Metalloproteinase, light chain
F: Metalloproteinase, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3564
Polymers48,1642
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-73 kcal/mol
Surface area19330 Å2
MethodPISA
4
A: Metalloproteinase, light chain
B: Metalloproteinase, heavy chain
hetero molecules

D: Metalloproteinase, light chain
C: Metalloproteinase, heavy chain
E: Metalloproteinase, light chain
F: Metalloproteinase, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,45216
Polymers144,4926
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-238 kcal/mol
Surface area53900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.095, 108.369, 86.466
Angle α, β, γ (deg.)90.00, 111.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Metalloproteinase, light chain


Mass: 23975.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Metalloproteinase, heavy chain


Mass: 24188.115 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M (NH4)2SO4, 25% PEG 4000, 15% Glycerol, 0.2M NDSB-211, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: Graphit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 72938 / Num. obs: 72501 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→41.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.242 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28789 3655 5 %RANDOM
Rwork0.22751 ---
obs0.23051 68819 98.49 %-
all-73585 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.12 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.18→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9410 0 50 5 9465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229740
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.95613319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84351275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11623.783341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.861151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051532
X-RAY DIFFRACTIONr_chiral_restr0.1420.21529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217342
X-RAY DIFFRACTIONr_mcbond_it1.0861.56398
X-RAY DIFFRACTIONr_mcangle_it1.973210275
X-RAY DIFFRACTIONr_scbond_it2.92833342
X-RAY DIFFRACTIONr_scangle_it4.5054.53044
LS refinement shellResolution: 2.185→2.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 244 -
Rwork0.293 4434 -
obs--87.5 %

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