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- PDB-7jr1: Crystal structure of the R64F mutant of Bauhinia Bauhinioides Kal... -

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Basic information

Entry
Database: PDB / ID: 7jr1
TitleCrystal structure of the R64F mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Bovine Trypsin
Components
  • Cationic trypsin
  • Kunitz-type inihibitor
KeywordsHYDROLASE/INHIBITOR / Human Kallikrein 4 / Bauhinia Bauhiniordes Kallikrein Inhibitor / Bovine Trypsin / R64F mutant / BbKI / STRUCTURAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
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. ...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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Kunitz-type inihibitor
Similarity search - Component
Biological speciesBauhinia bauhinioides (plant)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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 11, 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 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
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
G: Kunitz-type inihibitor
B: Cationic trypsin
C: Cationic trypsin
D: Cationic trypsin
E: Cationic trypsin
F: Cationic trypsin
H: Kunitz-type inihibitor
I: Kunitz-type inihibitor
J: Kunitz-type inihibitor
K: Kunitz-type inihibitor
L: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,89232
Polymers247,26312
Non-polymers1,62920
Water10,251569
1
A: Cationic trypsin
G: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4034
Polymers41,2112
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-38 kcal/mol
Surface area15370 Å2
MethodPISA
2
B: Cationic trypsin
H: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3073
Polymers41,2112
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-34 kcal/mol
Surface area15390 Å2
MethodPISA
3
C: Cationic trypsin
I: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4496
Polymers41,2112
Non-polymers2384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-52 kcal/mol
Surface area15350 Å2
MethodPISA
4
D: Cationic trypsin
J: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4995
Polymers41,2112
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-52 kcal/mol
Surface area15420 Å2
MethodPISA
5
E: Cationic trypsin
K: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6187
Polymers41,2112
Non-polymers4075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-62 kcal/mol
Surface area15380 Å2
MethodPISA
6
F: Cationic trypsin
L: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6187
Polymers41,2112
Non-polymers4075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-92 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.063, 207.063, 107.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein
Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Protein
Kunitz-type inihibitor


Mass: 17886.295 Da / Num. of mol.: 6 / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 1.6M Ammonium Sulfate, pH 4.2

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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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11-K, -H, -L20.5
ReflectionResolution: 2.05→89.66 Å / Num. obs: 163669 / % possible obs: 100 % / Redundancy: 11.5 % / Rsym value: 0.077 / Net I/σ(I): 18.1
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 8079 / Rsym value: 1.094

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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: 2.05→89.66 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.579 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1522 0.9 %RANDOM
Rwork0.1717 ---
obs0.1722 162115 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.2 Å2 / Biso mean: 45.9 Å2 / Biso min: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å2-0 Å2-0 Å2
2---4.09 Å2-0 Å2
3---8.18 Å2
Refinement stepCycle: final / Resolution: 2.05→89.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17334 0 84 569 17987
Biso mean--57.55 40.07 -
Num. residues----2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01317869
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716205
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6324309
X-RAY DIFFRACTIONr_angle_other_deg1.3311.57437881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.56552322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47524.098732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.908152883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7871548
X-RAY DIFFRACTIONr_chiral_restr0.0680.22322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023411
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 132 -
Rwork0.295 11933 -
all-12065 -
obs--99.9 %
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)
10.52360.52930.1250.6245-0.00570.3176-0.07820.01270.0513-0.07370.030.0760.00320.02950.04820.0962-0.01770.03560.04690.03580.071591.341184.300280.6848
20.07160.04280.05622.0641-0.38070.15690.0867-0.0290.0243-0.0388-0.1736-0.09370.0625-0.02030.08680.1147-0.01150.00240.0734-0.04130.0744130.785960.843187.2363
30.90410.6828-0.13340.5654-0.08770.156-0.1593-0.007-0.0063-0.12380.0785-0.0270.008-0.00190.08080.0956-0.0098-0.02090.1373-0.04860.0638115.808435.527180.7443
40.0940.0504-0.04641.34660.17260.16290.0770.0140.02570.0218-0.13610.0362-0.0080.00190.05910.1125-0.0160.0230.06180.03580.055576.523958.94287.1225
50.1770.02970.13340.9402-0.00760.21750.06850.0412-0.00410.0732-0.1462-0.02550.0049-0.0010.07760.1118-0.0278-0.02040.0808-0.0310.056627.30621.73685.8815
61.54461.13730.26781.09320.15650.0635-0.1145-0.13610.1348-0.1740.07260.09840.0215-0.04180.04190.1172-0.02350.02540.129-0.00160.0294-12.753223.830879.438
70.3172-0.0342-0.05041.34960.26840.1737-0.0615-0.00990.0905-0.03160.0849-0.07030.02240.0692-0.02330.1367-0.02890.01210.0436-0.00480.0582112.342106.765182.0903
81.14210.3328-0.14540.9647-0.13090.07760.10790.09390.13880.0839-0.0616-0.0156-0.0149-0.0051-0.04630.0674-0.05890.01050.0980.02210.0511139.629890.205385.056
90.47190.12250.16361.6056-0.44890.292-0.1063-0.0865-0.0915-0.07420.16660.0941-0.0354-0.052-0.06030.1079-0.01050.00640.06630.02610.045194.960112.93482.3958
101.10270.620.18410.81960.24110.14010.0540.0386-0.12650.0911-0.0447-0.00010.00930.0063-0.00920.0691-0.0605-0.01370.0662-0.00490.073367.50429.663184.6964
111.20610.4624-0.14291.0982-0.07140.13510.08740.08580.13530.077-0.0506-0.0646-0.0163-0.0554-0.03680.0882-0.05140.01030.07760.02130.037736.209731.105284.464
120.31710.05440.12421.74940.42070.4045-0.10090.00110.104-0.00420.1331-0.09790.01830.0561-0.03220.1261-0.0281-0.0330.0317-0.02280.05728.034346.353581.8408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 245
2X-RAY DIFFRACTION2B16 - 245
3X-RAY DIFFRACTION3C16 - 245
4X-RAY DIFFRACTION4D16 - 245
5X-RAY DIFFRACTION5E16 - 245
6X-RAY DIFFRACTION6F16 - 245
7X-RAY DIFFRACTION7G1 - 163
8X-RAY DIFFRACTION8H1 - 163
9X-RAY DIFFRACTION9I1 - 163
10X-RAY DIFFRACTION10J1 - 163
11X-RAY DIFFRACTION11K1 - 163
12X-RAY DIFFRACTION12L1 - 163

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