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- PDB-4h9w: crystal structure of a METHIONINE mutant of WCI -

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Basic information

Entry
Database: PDB / ID: 4h9w
Titlecrystal structure of a METHIONINE mutant of WCI
ComponentsChymotrypsin inhibitor 3
KeywordsHYDROLASE INHIBITOR / chymotrypsin inhibitor / inhibitor of chymotrypsin
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin inhibitor 3
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMajumder, S. / Sen, U.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: A conserved tryptophan (W91) at the barrel-lid junction modulates the packing and stability of Kunitz (STI) family of inhibitors.
Authors: Majumder, S. / Khamrui, S. / Banerjee, R. / Bhowmik, P. / Sen, U.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,6191
Polymers20,6191
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.632, 61.632, 211.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Chymotrypsin inhibitor 3 / WCI-3


Mass: 20619.318 Da / Num. of mol.: 1 / Mutation: W91M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10822
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.3M AMS, 5% GLYCEROL, 25% PEG 6K, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 2, 2011
RadiationMonochromator: graphaite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 8943 / Num. obs: 8893 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 7.05 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.1
Reflection shellHighest resolution: 2.5 Å / Redundancy: 7.05 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 7.1 / Num. unique all: 8943 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYL

1eyl


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 437 -RANDOM
Rwork0.2209 ---
all-8943 --
obs-8893 99.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 0 142 1520
LS refinement shellHighest resolution: 2.5 Å
RfactorNum. reflection
Rfree0.2565 437
Rwork0.2209 -
obs-8893

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