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- PDB-7jrx: Crystal structure of the R64F mutant of Bauhinia Bauhinioides com... -

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Basic information

Entry
Database: PDB / ID: 7jrx
TitleCrystal structure of the R64F mutant of Bauhinia Bauhinioides complexed with Bovine Chymotrypsin
Components
  • Chymotrypsin A chain A
  • Chymotrypsin A chain B
  • Chymotrypsin A chain C
  • Kunitz-type inihibitor
KeywordsHYDROLASE/INHIBITOR / Bovine Chymotrypsin / R64F / Bauhinia Bauhinioides Kallikrein Inhibitor / STRUCTURAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


chymotrypsin / endopeptidase inhibitor activity / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. ...Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chymotrypsinogen A / Kunitz-type inihibitor
Similarity search - Component
Biological speciesBauhinia bauhinioides (plant)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI.
Authors: Li, M. / Srp, J. / Mares, M. / Wlodawer, A. / Gustchina, A.
History
DepositionAug 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
I: Kunitz-type inihibitor
a: Chymotrypsin A chain A
b: Chymotrypsin A chain B
c: Chymotrypsin A chain C
i: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)86,7868
Polymers86,7868
Non-polymers00
Water13,926773
1
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
I: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)43,3934
Polymers43,3934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-75 kcal/mol
Surface area16160 Å2
MethodPISA
2
a: Chymotrypsin A chain A
b: Chymotrypsin A chain B
c: Chymotrypsin A chain C
i: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)43,3934
Polymers43,3934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-74 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.018, 60.693, 425.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A,B
21a,b
12C
22c
13I
23i

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1110A1 - 13
2110a1 - 13
1020C149 - 245
2020c149 - 245
1030I1 - 163
2030i1 - 163
1210B16 - 146
221b16 - 146

NCS ensembles :
ID
1
2
3

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Components

#1: Protein/peptide Chymotrypsin A chain A


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein Chymotrypsin A chain B


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein Chymotrypsin A chain C


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein Kunitz-type inihibitor


Mass: 18130.498 Da / Num. of mol.: 2 / Mutation: R64F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2M Ammonium Acetate at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→85.11 Å / Num. obs: 73379 / % possible obs: 95 % / Redundancy: 6.4 % / Rsym value: 0.096 / Net I/σ(I): 12.4
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 2276 / Rsym value: 0.153

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→71.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.68 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1451 2 %RANDOM
Rwork0.1755 ---
obs0.1761 71824 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 239.55 Å2 / Biso mean: 20.979 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0 Å2
2---0.06 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.77→71.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 0 773 6816
Biso mean---31.19 -
Num. residues----807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136283
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175790
X-RAY DIFFRACTIONr_angle_refined_deg1.661.6348576
X-RAY DIFFRACTIONr_angle_other_deg1.4311.57513506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6625817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89224.023256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0951518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A40850.05
12a40850.05
11B40850.05
12b40850.05
21C26210.07
22c26210.07
31I46930.11
32i46930.11
LS refinement shellResolution: 1.77→1.811 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.392 69 -
Rwork0.277 3189 -
obs--58.37 %

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