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- PDB-2bea: Crystal structure of Asn14 to Gly mutant of WCI -

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Basic information

Entry
Database: PDB / ID: 2bea
TitleCrystal structure of Asn14 to Gly mutant of WCI
ComponentsChymotrypsin inhibitor 3
KeywordsHYDROLASE INHIBITOR / Beta trefoil / spacer / mutant
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: 2.35 Å
AuthorsDattagupta, J.K. / Sen, U. / Dasgupta, J. / Khamrui, S.
Citation
Journal: Biochemistry / Year: 2006
Title: Spacer Asn Determines the Fate of Kunitz (STI) Inhibitors, as Revealed by Structural and Biochemical Studies on WCI Mutants.
Authors: Dasgupta, J. / Khamrui, S. / Dattagupta, J.K. / Sen, U.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Single mutation at P1 of a chymotrypsin inhibitor changes it to a trypsin inhibitor: X-ray structural (2.15 A) and biochemical basis.
Authors: Khamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U.
History
DepositionOct 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin inhibitor 3
B: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)41,2352
Polymers41,2352
Non-polymers00
Water5,080282
1
A: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,6171
Polymers20,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,6171
Polymers20,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.300, 40.443, 58.778
Angle α, β, γ (deg.)85.97, 80.00, 85.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chymotrypsin inhibitor 3 / WCI-3


Mass: 20617.279 Da / Num. of mol.: 2 / Mutation: N14G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.976368 Å3/Da / Density % sol: 37.764629 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→15 Å / Num. all: 12855 / Num. obs: 11423 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.044

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→14.77 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 752257 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 590 5.2 %RANDOM
Rwork0.211 ---
obs0.211 11423 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2231 Å2 / ksol: 0.281937 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å2-1.87 Å211.68 Å2
2---10.46 Å2-4.62 Å2
3---6.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.35→14.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 0 282 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.31.5
X-RAY DIFFRACTIONc_mcangle_it9.792
X-RAY DIFFRACTIONc_scbond_it7.992
X-RAY DIFFRACTIONc_scangle_it11.492.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.454 86 5.7 %
Rwork0.363 1420 -
obs--70.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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