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- PDB-4zot: Crystal structure of BbKI, a disulfide-free plasma kallikrein inh... -

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Basic information

Entry
Database: PDB / ID: 4zot
TitleCrystal structure of BbKI, a disulfide-free plasma kallikrein inhibitor at 1.4 A resolution
ComponentsKunitz-type serine protease inhibitor BbKI
KeywordsPROTEIN BINDING / kallikrein inhibitor / Kunitz-type kallikrein inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Kunitz-type serine protease inhibitor BbKI
Similarity search - Component
Biological speciesBauhinia bauhinioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShabalin, I.G. / Zhou, D. / Wlodawer, A. / Oliva, M.L.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of BbKI, a disulfide-free plasma kallikrein inhibitor.
Authors: Zhou, D. / Hansen, D. / Shabalin, I.G. / Gustchina, A. / Vieira, D.F. / de Brito, M.V. / Araujo, A.P. / Oliva, M.L. / Wlodawer, A.
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 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: Kunitz-type serine protease inhibitor BbKI


Theoretical massNumber of molelcules
Total (without water)18,3661
Polymers18,3661
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.736, 59.462, 64.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kunitz-type serine protease inhibitor BbKI


Mass: 18365.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: rBbKI in 0.05 M Tris/HCl, pH 8.0, and 0.15 M NaCl was concentrated to 6.3 mg/ml and crystallized using the conditions 8% PEG 4000, 0.1 M sodium acetate, pH 4.6. Cryoprotectant solution - ...Details: rBbKI in 0.05 M Tris/HCl, pH 8.0, and 0.15 M NaCl was concentrated to 6.3 mg/ml and crystallized using the conditions 8% PEG 4000, 0.1 M sodium acetate, pH 4.6. Cryoprotectant solution - mother liquor with extra 25% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 34445 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.024 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Χ2: 0.958 / Net I/av σ(I): 32.805 / Net I/σ(I): 10.2 / Num. measured all: 171809
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.424.80.6281.916310.7520.3110.7040.63593.3
1.42-1.4550.51916630.8150.2540.5810.6594
1.45-1.4850.46916570.8330.2280.5240.66494.9
1.48-1.515.10.37616810.9040.1810.420.6993.8
1.51-1.5450.31516780.9190.1540.3530.69696.2
1.54-1.585.10.25516760.9420.1240.2850.70494.7
1.58-1.6250.20916920.9610.1010.2340.69595
1.62-1.6650.17917010.9690.0870.2010.7596.3
1.66-1.715.10.14617040.9780.0710.1630.76595.7
1.71-1.7650.11716970.9860.0570.1310.81896.2
1.76-1.8350.09517230.990.0460.1060.84996.6
1.83-1.950.07517280.9950.0370.0840.86296.8
1.9-1.9950.06217490.9950.030.0690.96497.2
1.99-2.0950.05317290.9960.0260.061.01297
2.09-2.2250.05117390.9960.0250.0581.22196.9
2.22-2.3950.04917610.9960.0240.0551.33598.3
2.39-2.634.90.04417750.9960.0220.0491.30797.8
2.63-3.024.90.03818010.9980.0190.0421.28998.5
3.02-3.84.90.03418190.9980.0160.0381.48397.8
3.8-504.80.03418410.9970.0170.0391.66693.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GO2

2go2


Resolution: 1.4→43.57 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1634 / WRfactor Rwork: 0.1235 / FOM work R set: 0.8947 / SU B: 1.823 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0503 / SU Rfree: 0.0519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1665 1726 5 %RANDOM
Rwork0.1226 ---
obs0.1247 32686 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.6 Å2 / Biso mean: 23.091 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.4→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 213 1461
Biso mean---40.52 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191358
X-RAY DIFFRACTIONr_bond_other_d0.0040.021311
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9731864
X-RAY DIFFRACTIONr_angle_other_deg1.8633049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6455182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02224.03557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19715231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.965157
X-RAY DIFFRACTIONr_chiral_restr0.1690.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_mcbond_it2.9431.935678
X-RAY DIFFRACTIONr_mcbond_other2.94167.566677
X-RAY DIFFRACTIONr_mcangle_it3.6562.906853
X-RAY DIFFRACTIONr_rigid_bond_restr2.81731358
X-RAY DIFFRACTIONr_sphericity_free29.7520.169
X-RAY DIFFRACTIONr_sphericity_bonded16.4850.11458
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 128 -
Rwork0.229 2284 -
all-2412 -
obs--92.95 %

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