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- PDB-4tlp: Crystal structure of a alanine91 mutant of WCI -

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Basic information

Entry
Database: PDB / ID: 4tlp
TitleCrystal structure of a alanine91 mutant of WCI
ComponentsChymotrypsin inhibitor 3
KeywordsHYDROLASE / Inhibitor / Chymotrypsin inhibitor / Tryptophan
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSen, U. / Majumder, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Atomic Energy India
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
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references / Structure summary
Revision 1.2Dec 24, 2014Group: Database references
Revision 2.0Feb 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / refine_hist / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Sep 27, 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
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: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)19,3411
Polymers19,3411
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.290, 69.950, 70.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chymotrypsin inhibitor 3 / WCI-3


Mass: 19340.973 Da / Num. of mol.: 1 / Fragment: UNP residues 26-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Production host: Atlantibacter hermannii (bacteria) / References: UniProt: P10822
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 30% PEG6000, 0.1M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→35.165 Å / Num. obs: 14305 / % possible obs: 100 % / Redundancy: 14.2 % / Net I/σ(I): 16.5
Reflection shellHighest resolution: 1.9 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 16.5 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYL

1eyl


Resolution: 1.9→35.165 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 719 5.03 %
Rwork0.1707 --
obs0.1725 14305 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→35.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 129 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071398
X-RAY DIFFRACTIONf_angle_d1.2251900
X-RAY DIFFRACTIONf_dihedral_angle_d15.276525
X-RAY DIFFRACTIONf_chiral_restr0.122213
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04670.26921550.19342645X-RAY DIFFRACTION100
2.0467-2.25260.22841330.17652682X-RAY DIFFRACTION100
2.2526-2.57850.25181320.1822686X-RAY DIFFRACTION100
2.5785-3.24830.2261430.18042726X-RAY DIFFRACTION100
3.2483-35.17110.16751560.15652847X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1837-0.08390.5832.74770.12461.8620.08420.1009-0.1242-0.30820.00550.00870.0665-0.0378-0.06970.2171-0.0095-0.00850.192-0.01720.2091-1.40196.51417.9926
21.11481.1478-0.01673.9853-0.14151.7061-0.02320.178-0.0338-0.564-0.0078-0.14540.02840.0524-0.00530.180.02310.02070.17920.00680.12390.815211.963613.9328
31.39730.09820.40111.72320.681.3673-0.0093-0.1674-0.02050.1141-0.14670.33980.082-0.3420.0870.1179-0.01280.01470.1779-0.0190.1797-5.282114.416326.3478
41.76861.0424-0.30642.52480.20032.00280.1077-0.02180.22320.0703-0.12870.151-0.1484-0.15510.06460.1190.0193-0.00960.1374-0.01820.1491-0.168119.877424.678
55.15582.20593.51413.3003-0.94084.85720.33060.7637-0.1502-0.52980.1966-1.49910.66190.8472-0.30990.25820.08930.12860.3312-0.0410.454912.05135.229714.1786
62.6218-1.31110.62043.11781.74272.29150.0481-0.0709-0.07210.4937-0.0951-0.45570.09040.18780.05550.18990.0155-0.0460.1570.00960.07385.362311.303629.6046
73.77140.44810.63133.64031.66814.4364-0.1431-0.2854-0.19120.33880.0172-0.34520.51140.1288-0.00670.33840.03480.04580.2050.00340.33925.40434.358220.3467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 179 )

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