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- PDB-6dwh: Crystal structure of complex of BBKI and Bovine Trypsin -

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Basic information

Entry
Database: PDB / ID: 6dwh
TitleCrystal structure of complex of BBKI and Bovine Trypsin
Components
  • Cationic trypsin
  • Kunitz-type inihibitor
KeywordsHYDROLASE
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / : / Serine proteases, trypsin family, histidine active site / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLi, M. / Wlodawer, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes.
Authors: Li, M. / Srp, J. / Gustchina, A. / Dauter, Z. / Mares, M. / Wlodawer, A.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)254,91322
Polymers254,65812
Non-polymers25510
Water14,592810
1
D: Cationic trypsin
J: Kunitz-type inihibitor
hetero molecules

A: Cationic trypsin
G: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)84,9446
Polymers84,8864
Non-polymers582
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
Buried area6200 Å2
ΔGint-42 kcal/mol
Surface area28370 Å2
MethodPISA
2
C: Cationic trypsin
I: Kunitz-type inihibitor
hetero molecules

B: Cationic trypsin
H: Kunitz-type inihibitor


Theoretical massNumber of molelcules
Total (without water)84,9557
Polymers84,8864
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Buried area6290 Å2
ΔGint-60 kcal/mol
Surface area28360 Å2
MethodPISA
3
F: Cationic trypsin
L: Kunitz-type inihibitor
hetero molecules

E: Cationic trypsin
K: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0139
Polymers84,8864
Non-polymers1275
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/31
Buried area6660 Å2
ΔGint-78 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.809, 207.809, 107.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / Fragment: residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein
Kunitz-type inihibitor


Mass: 19118.688 Da / Num. of mol.: 6 / Fragment: residues 19-193
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M Ammonium Sulfate 0.1M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 14, 2017
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, L10.479
11-K, -H, -L20.521
ReflectionResolution: 2→50 Å / Num. obs: 169571 / % possible obs: 96.5 % / Redundancy: 5.6 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Rsym value: 0.099 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 6265 / Rpim(I) all: 0.893 / Rrim(I) all: 1.43 / Rsym value: 1.105 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: SAD
Starting model: 6DWF

6dwf


Resolution: 2→49.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.628 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22282 1397 1 %RANDOM
Rwork0.18991 ---
obs0.19024 140125 80.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.436 Å2
Baniso -1Baniso -2Baniso -3
1--5.22 Å2-0 Å2-0 Å2
2---5.22 Å2-0 Å2
3---10.44 Å2
Refinement stepCycle: 1 / Resolution: 2→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17334 0 10 810 18154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01917772
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216212
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.95624096
X-RAY DIFFRACTIONr_angle_other_deg1.129337884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91452286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27225684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.104152904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9291554
X-RAY DIFFRACTIONr_chiral_restr0.0780.22694
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9232.29234
X-RAY DIFFRACTIONr_mcbond_other0.9232.1999233
X-RAY DIFFRACTIONr_mcangle_it1.7273.29511472
X-RAY DIFFRACTIONr_mcangle_other1.7273.29511473
X-RAY DIFFRACTIONr_scbond_it0.5552.2558536
X-RAY DIFFRACTIONr_scbond_other0.5552.2558537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.073.35512618
X-RAY DIFFRACTIONr_long_range_B_refined5.36126.03519224
X-RAY DIFFRACTIONr_long_range_B_other5.36126.03719225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 8 -
Rwork0.258 567 -
obs--4.43 %
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)
10.57370.34540.10290.5721-0.15830.2702-0.1089-0.08460.0234-0.15660.06310.03340.0346-0.00530.04580.1342-0.02320.03630.09980.03060.047491.86284.683381.0128
20.86170.78580.45292.9768-0.16750.61960.19-0.0053-0.0749-0.0138-0.1881-0.12130.05320.0353-0.00190.1136-0.0051-0.01810.0954-0.02540.0228131.097960.922987.2667
30.49490.5253-0.02420.6923-0.01010.214-0.1348-0.0630.0269-0.1920.07040.0043-0.0203-0.01160.06440.1523-0.0177-0.04610.1489-0.04090.0436115.999335.677580.9564
40.78750.6082-0.38711.7152-0.12330.56970.1565-0.02330.10530.0653-0.11240.13020.0003-0.0044-0.04410.1106-0.0320.01710.06780.0180.029276.990859.286587.2933
50.37750.39650.44481.55970.09790.84090.1414-0.06620.03590.1575-0.2283-0.04180.0346-0.04380.08680.1458-0.04630.01570.1119-0.03040.025427.27892.042185.0087
60.83150.94540.02892.5371-0.45640.9338-0.0887-0.05060.1307-0.19360.09860.15610.01320.0236-0.00990.1002-0.0318-0.00880.07780.00710.0279-12.774523.594678.7599
70.95090.07380.03841.54560.36080.1976-0.0679-0.08810.0469-0.07420.0606-0.09460.01960.04070.00730.1309-0.00010.0190.0496-0.00020.0163112.7846107.316682.0668
81.15830.8857-0.77641.299-0.81371.06190.1085-0.00270.14830.1143-0.06650.0259-0.0517-0.0402-0.0420.07160.0044-0.00030.1048-0.00770.0363140.126590.245585.0475
90.9525-0.0357-0.05022.1678-0.55560.2461-0.1265-0.1354-0.1256-0.04690.12680.1308-0.0063-0.0041-0.00030.12990.0137-0.00560.09520.00820.038895.246412.979582.5267
101.15960.59090.36520.91770.62140.88130.0737-0.0215-0.14450.1291-0.0413-0.04820.08240.0516-0.03240.0747-0.0244-0.00430.08110.01740.02767.788730.015584.7446
111.44160.2907-0.19861.5434-0.22230.29880.06840.0210.16420.0097-0.1175-0.05780.0192-0.02650.04910.0629-0.04940.01350.1284-0.00750.039836.495731.443284.0752
120.42440.2390.45321.75850.34381.004-0.06050.04880.0401-0.09830.0493-0.14190.01420.08560.01120.1006-0.00020.00410.05610.00090.0227.874546.259981.43
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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