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- PDB-3vwc: High resolution structure of proteinase inhibitor from Coprinopsi... -

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Basic information

Entry
Database: PDB / ID: 3vwc
TitleHigh resolution structure of proteinase inhibitor from Coprinopsis cinerea
ComponentsSerine protease inhibitor 1
KeywordsHYDROLASE INHIBITOR / sulphur SAD phasing / beta trefoil / inhibitor / serine proteases
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 / SAD / Resolution: 1.5 Å
AuthorsRenko, M. / Sabotic, J. / Turk, D.
CitationJournal: To be Published
Title: High resolution structure of proteinase inhibitor from Coprinopsis cinerea
Authors: Renko, M. / Sabotic, J. / Turk, D.
History
DepositionAug 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7182
Polymers16,6001
Non-polymers1181
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.626, 38.243, 54.890
Angle α, β, γ (deg.)90.000, 96.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine protease inhibitor 1


Mass: 16599.549 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 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: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.49→55 Å / Num. all: 26452 / Num. obs: 26279 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.49→1.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
PROTEUM2data collection
PROTEUM2data reduction
PROTEUM2data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→54.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8257 / SU B: 1.526 / SU ML: 0.058 / SU R Cruickshank DPI: 0.083 / SU Rfree: 0.0859 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1326 5.1 %RANDOM
Rwork0.1991 ---
obs0.201 26196 99.13 %-
all-26452 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.93 Å2 / Biso mean: 19.6392 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→54.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 8 234 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221227
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9711690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9925158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16924.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80615197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.389157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022953
X-RAY DIFFRACTIONr_mcbond_it2.1941.5754
X-RAY DIFFRACTIONr_mcangle_it3.27521240
X-RAY DIFFRACTIONr_scbond_it4.4133473
X-RAY DIFFRACTIONr_scangle_it6.7274.5443
LS refinement shellResolution: 1.495→1.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 96 -
Rwork0.279 1704 -
all-1800 -
obs--92.59 %

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