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- PDB-2et2: Crystal structure of an Asn to Ala mutant of Winged Bean Chymotry... -

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Basic information

Entry
Database: PDB / ID: 2et2
TitleCrystal structure of an Asn to Ala mutant of Winged Bean Chymotrypsin Inhibitor protein
ComponentsChymotrypsin inhibitor 3
KeywordsHYDROLASE INHIBITOR / Beta trefoil / mutation / scaffold
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
NICKEL (II) ION / Chymotrypsin inhibitor 3
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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.
#2: Journal: Protein Eng. / Year: 2003
Title: In silico mutations and molecular dynamics studies on a winged bean chymotrypsin inhibitor protein.
Authors: Dasgupta, J. / Sen, U. / Dattagupta, J.K.
History
DepositionOct 27, 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: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7863
Polymers20,6311
Non-polymers1552
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Chymotrypsin inhibitor 3
hetero molecules

A: Chymotrypsin inhibitor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5726
Polymers41,2632
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area1730 Å2
ΔGint-69 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.393, 60.393, 212.180
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: 20631.307 Da / Num. of mol.: 1 / Mutation: N17A
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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25.5% PEG 8K, 0.17 M Ammonium Sulphate, 15% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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: Mar 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→19.93 Å / Num. all: 14217 / Num. obs: 13870 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.2 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1910373.47 / 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
Rfree0.275 693 5 %RANDOM
Rwork0.227 ---
obs0.227 13870 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.5083 Å2 / ksol: 0.358243 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å24.38 Å20 Å2
2--3.83 Å20 Å2
3----7.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 6 217 1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.711.5
X-RAY DIFFRACTIONc_mcangle_it4.32
X-RAY DIFFRACTIONc_scbond_it4.222
X-RAY DIFFRACTIONc_scangle_it6.972.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 128 5.8 %
Rwork0.267 2075 -
obs--96 %
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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