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- PDB-1wni: Crystal Structure of H2-Proteinase -

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Basic information

Entry
Database: PDB / ID: 1wni
TitleCrystal Structure of H2-Proteinase
ComponentsTrimerelysin II
KeywordsHYDROLASE / METALLOPROTEASE / ZINC / METZINCIN / SNAKE VENOM
Function / homology
Function and homology information


trimerelysin II / metalloendopeptidase activity / extracellular region / metal ion binding
Similarity search - Function
Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Snake venom metalloproteinase trimerelysin-2
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsKumasaka, T. / Yamamoto, M. / Moriyama, H. / Tanaka, N. / Sato, M. / Katsube, Y. / Yamakawa, Y. / Omori-Satoh, T. / Iwanaga, S. / Ueki, T.
Citation
Journal: J.Biochem. / Year: 1996
Title: Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
Authors: Kumasaka, T. / Yamamoto, M. / Moriyama, H. / Tanaka, N. / Sato, M. / Katsube, Y. / Yamakawa, Y. / Omori-Satoh, T. / Iwanaga, S. / Ueki, T.
#1: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Crystallization and preliminary X-ray study of H2-proteinase from the venom of Trimeresurus flavoviridis
Authors: Kumasaka, T. / Takeya, H. / Yamamoto, M. / Yamakawa, Y. / Omori-Satoh, T. / Moriyama, H. / Tanaka, N. / Sato, M. / Katsube, Y. / Iwanaga, S.
History
DepositionAug 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimerelysin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1112
Polymers23,0461
Non-polymers651
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.800, 77.800, 82.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Trimerelysin II / H2-PROTEINASE / H2 metalloproteinase


Mass: 23045.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / References: UniProt: P20165, trimerelysin II
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.07 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 14262 / Num. obs: 14262 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
WEISdata reduction
MLPHAREphasing
X-PLOR3.851refinement
WEISdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.176 10635
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 1 78 1670

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