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- PDB-3n0k: Proteinase inhibitor from Coprinopsis cinerea -

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Basic information

Entry
Database: PDB / ID: 3n0k
TitleProteinase inhibitor from Coprinopsis cinerea
ComponentsSerine protease inhibitor 1
KeywordsHydrolase Inhibitor / Proteinase inhibitor
Function / homologyPeptidase inhibitor I66 / Peptidase inhibitor I66 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / serine-type endopeptidase inhibitor activity / Mainly Beta / Serine protease inhibitor 1
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRenko, M. / Sabotic, J. / Bleuler-Martinez, S. / Kallert, S. / Avanzo, P. / Kos, J. / Aebi, M. / Kuenzler, M. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis of Trypsin Inhibition and Entomotoxicity of Cospin, Serine Protease Inhibitor Involved in Defense of Coprinopsis cinerea Fruiting Bodies.
Authors: Sabotic, J. / Bleuler-Martinez, S. / Renko, M. / Avanzo Caglic, P. / Kallert, S. / Strukelj, B. / Turk, D. / Aebi, M. / Kos, J. / Kunzler, M.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
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
A: Serine protease inhibitor 1


Theoretical massNumber of molelcules
Total (without water)16,7311
Polymers16,7311
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.631, 38.192, 55.078
Angle α, β, γ (deg.)90.000, 96.870, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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Components

#1: Protein Serine protease inhibitor 1


Mass: 16730.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Plasmid: pet24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0EWJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES buffer, 20% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2009 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→16.87 Å / Num. all: 15292 / Num. obs: 14500 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.034 / Χ2: 2.396 / Net I/σ(I): 51.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Num. unique all: 621 / Χ2: 3.508 / % possible all: 83.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
AMoREphasing
MAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→16.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.88 / SU B: 2.207 / SU ML: 0.071 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 727 5 %RANDOM
Rwork0.168 ---
obs0.169 14500 94.84 %-
all-15292 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.86 Å2 / Biso mean: 23.282 Å2 / Biso min: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0.59 Å2
2---0.07 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→16.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 0 251 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221203
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9631645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80725.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.102156
X-RAY DIFFRACTIONr_chiral_restr0.1430.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022940
X-RAY DIFFRACTIONr_mcbond_it1.2011.5749
X-RAY DIFFRACTIONr_mcangle_it2.04921221
X-RAY DIFFRACTIONr_scbond_it2.9673454
X-RAY DIFFRACTIONr_scangle_it4.8724.5424
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 41 -
Rwork0.285 914 -
all-955 -
obs--86.11 %

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