[English] 日本語
Yorodumi
- PDB-6dwh: Crystal structure of complex of BBKI and Bovine Trypsin -

+
Open data


ID or keywords:

Loading...

-
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 / Peptidase S1A, chymotrypsin family ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more