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- PDB-2go2: Crystal structure of BbKI, a Kunitz-type kallikrein inhibitor -

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Basic information

Entry
Database: PDB / ID: 2go2
TitleCrystal structure of BbKI, a Kunitz-type kallikrein inhibitor
ComponentsKunitz-type serine protease inhibitor BbKI
KeywordsPROTEIN BINDING / BETA-TREFOIL FOLD
Function / homology
Function and homology information


endopeptidase inhibitor activity / 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 / Kunitz-type inihibitor
Similarity search - Component
Biological speciesBauhinia bauhinioides (plant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.87 Å
AuthorsNavarro, M.V.A.S. / Garratt, R.C.
Citation
Journal: To be Published / Year: 2006
Title: The Crystal Structure of BbKI, a kunitz-type kallikrein inhibitor devoid of disulfide bridges
Authors: Navarro, M.V.A.S. / Oliva, M.L.V. / Araujo, A.P.U. / Garratt, R.C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides
Authors: Navarro, M.V. / Vierira, D.F. / Nagem, R.A. / de Araujo, A.P. / Oliva, M.L. / Garratt, R.C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Getting the most out of X-ray home sources
Authors: Nagem, R.A. / Ambrosio, A.L. / Rojas, A.L. / Navarro, M.V. / Golubev, A.M. / Garratt, R.C. / Polikarpov, I.
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz-type serine protease inhibitor BbKI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9633
Polymers17,8391
Non-polymers1242
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.701, 64.143, 59.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit of the crystal contains a monomer, which represents the biological assembly

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Components

#1: Protein Kunitz-type serine protease inhibitor BbKI


Mass: 17839.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Gene: BbKI / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83052, UniProt: Q6VEQ7*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8%(w/v) PEG 4000, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→26.44 Å / Num. obs: 14628 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 32.8
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 10.7 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→19.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.2 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20974 734 5 %RANDOM
Rwork0.16579 ---
obs0.16799 13850 95.66 %-
all-13850 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 8 160 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221349
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.9731842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.2025178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73523.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.848158
X-RAY DIFFRACTIONr_chiral_restr0.1730.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021037
X-RAY DIFFRACTIONr_nbd_refined0.210.2583
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_mcbond_it1.671.5864
X-RAY DIFFRACTIONr_mcangle_it2.50821368
X-RAY DIFFRACTIONr_scbond_it3.4973552
X-RAY DIFFRACTIONr_scangle_it5.3764.5467
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 51 -
Rwork0.204 942 -
obs-942 91.77 %
Refinement TLS params.Method: refined / Origin x: 42.901 Å / Origin y: 58.142 Å / Origin z: 7.866 Å
111213212223313233
T-0.0287 Å20.0025 Å2-0.0031 Å2--0.0642 Å2-0.0166 Å2---0.0833 Å2
L1.7105 °2-0.1362 °2-0.4099 °2-1.2553 °20.5183 °2--1.3936 °2
S0.0335 Å °-0.1197 Å °0.1516 Å °0.0575 Å °0.0077 Å °-0.0257 Å °-0.0217 Å °-0.0055 Å °-0.0412 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1631 - 163
2X-RAY DIFFRACTION1AB - C700 - 701

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