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- PDB-1yp1: Crystal structure of a non-hemorrhagic fibrin(ogen)olytic metallo... -

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Basic information

Entry
Database: PDB / ID: 1yp1
TitleCrystal structure of a non-hemorrhagic fibrin(ogen)olytic metalloproteinase from venom of Agkistrodon acutus
Components
  • FII
  • KNL
KeywordsHYDROLASE / FII crystal structure
Function / homologyCollagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLou, Z. / Hou, J. / Chen, J. / Liang, X. / Qiu, P. / Liu, Y. / Li, M. / Rao, Z.
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of a non-hemorrhagic fibrin(ogen)olytic metalloproteinase complexed with a novel natural tri-peptide inhibitor from venom of Agkistrodon acutus
Authors: Lou, Z. / Hou, J. / Liang, X. / Chen, J. / Qiu, P. / Liu, Y. / Li, M. / Rao, Z. / Yan, G.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FII
B: KNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4273
Polymers22,3622
Non-polymers651
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-43 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.565, 80.565, 66.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein FII


Mass: 21987.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin)
References: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide KNL


Mass: 374.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally synthesis
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2004
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23498 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.86→1.94 Å / % possible all: 90.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 18667 random
Rwork0.217 --
all0.219 20099 -
obs0.219 19624 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 1 124 1663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_bond_d0.012

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