[English] 日本語
Yorodumi
- PDB-7qiq: CRYSTAL STRUCTURE OF THE P1 aminobutanoic acid (ABU) BPTI MUTANT-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qiq
TitleCRYSTAL STRUCTURE OF THE P1 aminobutanoic acid (ABU) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX
Components
  • (Chymotrypsin A chain ...) x 3
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE / CHYMOTRYPSIN / SERINE PROTEINASE / BOVINE PANCREATIC TRYPSIN INHIBITOR / BPTI / PROTEIN-PROTEIN INTERACTION / S1 POCKET / PRIMARY SPECIFICITY / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymotrypsin / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serpin family protein binding ...chymotrypsin / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
: / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...: / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chymotrypsinogen A / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDimos, N. / Leppkes, J. / Koksch, B. / Wahl, M.C. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Project-ID 387284271 Germany
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Fluorine-induced polarity increases inhibitory activity of BPTI towards chymotrypsin.
Authors: Leppkes, J. / Dimos, N. / Loll, B. / Hohmann, T. / Dyrks, M. / Wieseke, A. / Keller, B.G. / Koksch, B.
History
DepositionDec 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin A chain A
B: Chymotrypsin A chain B
C: Chymotrypsin A chain C
D: Pancreatic trypsin inhibitor
E: Chymotrypsin A chain A
F: Chymotrypsin A chain B
G: Chymotrypsin A chain C
H: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,60452
Polymers63,4928
Non-polymers4,11244
Water8,935496
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.435, 100.435, 206.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain 'A' and resid 1 through 13) and (chain 'B'...
d_2ens_1(chain 'E' and resid 1 through 13) and (chain 'F'...
d_1ens_2(chain 'D' and (resid 1 through 10 or resid 12...
d_2ens_2(chain 'G' and (resid 1 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
d_11ens_1A1 - 10
d_12ens_1A12 - 13
d_13ens_1B - A15 - 44
d_14ens_1B - A46 - 48
d_15ens_1B - A50 - 60
d_16ens_1B62 - 70
d_17ens_1B72 - 77
d_18ens_1B79 - 85
d_19ens_1B87 - 91
d_110ens_1B93 - 94
d_111ens_1B96 - 120
d_112ens_1B122 - 124
d_113ens_1B126 - 146
d_114ens_1C149 - 159
d_115ens_1C162 - 183
d_116ens_1C185
d_117ens_1C187 - 211
d_118ens_1C213 - 217
d_119ens_1C219 - 221
d_120ens_1C223 - 239
d_21ens_1E1 - 10
d_22ens_1E12 - 13
d_23ens_1F15 - 44
d_24ens_1F46 - 48
d_25ens_1F50 - 60
d_26ens_1F62 - 70
d_27ens_1F72 - 77
d_28ens_1F79 - 85
d_29ens_1F87 - 91
d_210ens_1F93 - 94
d_211ens_1F96 - 120
d_212ens_1F122 - 124
d_213ens_1F126 - 146
d_214ens_1G149 - 159
d_215ens_1G162 - 183
d_216ens_1G185
d_217ens_1G187 - 211
d_218ens_1G213 - 217
d_219ens_1G219 - 221
d_220ens_1G223 - 239
d_11ens_2D1 - 10
d_12ens_2D12 - 16
d_13ens_2D18 - 25
d_14ens_2D27 - 30
d_15ens_2D32 - 58
d_21ens_2H1 - 10
d_22ens_2H12 - 16
d_23ens_2H18 - 25
d_24ens_2H27 - 30
d_25ens_2H32 - 58

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.362266290596, -0.932074638958, 4.59354405157E-5), (-0.931908333129, 0.362200721251, -0.0189075691185), (0.01760662781, -0.00689238254854, -0.999821234881)-12.2446999173, -8.14697328288, 29.3454831602
2given(-0.365087958761, -0.930970506541, 0.00216756047163), (-0.930916234229, 0.365038978776, -0.0118957481293), (0.0102833466006, -0.00636081163418, -0.999926893757)-12.1211205877, -8.06199643715, 29.5509489825

-
Components

-
Chymotrypsin A chain ... , 3 types, 6 molecules AEBFCG

#1: Protein/peptide Chymotrypsin A chain A


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766
#2: Protein Chymotrypsin A chain B


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766
#3: Protein Chymotrypsin A chain C


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766

-
Protein , 1 types, 2 molecules DH

#4: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPI / BPTI


Mass: 6483.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P00974

-
Non-polymers , 3 types, 540 molecules

#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M ammonium sulfate and 0.1 M MES/NaOH (pH 6.5).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2021
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 100371 / % possible obs: 99.6 % / Redundancy: 11.7 % / Biso Wilson estimate: 38.4 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.135 / Net I/σ(I): 12.95
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 15880 / CC1/2: 0.671 / Rrim(I) all: 2.16 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8N

1t8n


Resolution: 1.85→32.88 Å / SU ML: 0.2843 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 2097 2.09 %
Rwork0.1609 98166 -
obs0.1615 100263 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 249 496 5157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01395051
X-RAY DIFFRACTIONf_angle_d1.1366875
X-RAY DIFFRACTIONf_chiral_restr0.076747
X-RAY DIFFRACTIONf_plane_restr0.0083870
X-RAY DIFFRACTIONf_dihedral_angle_d13.50041788
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.315093052659
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.205150702906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.481320.37636190X-RAY DIFFRACTION94.37
1.89-1.940.29751400.30886552X-RAY DIFFRACTION99.93
1.94-1.990.29271390.25476525X-RAY DIFFRACTION99.88
1.99-2.050.25581410.22496615X-RAY DIFFRACTION99.9
2.05-2.110.25091390.20496497X-RAY DIFFRACTION99.94
2.11-2.190.21371400.19066573X-RAY DIFFRACTION99.91
2.19-2.280.22991400.18116561X-RAY DIFFRACTION99.85
2.28-2.380.21421410.16866564X-RAY DIFFRACTION99.87
2.38-2.50.20761400.16376570X-RAY DIFFRACTION99.96
2.5-2.660.18851410.15236579X-RAY DIFFRACTION99.97
2.66-2.870.18581410.15446586X-RAY DIFFRACTION99.94
2.87-3.150.16511400.1566555X-RAY DIFFRACTION100
3.16-3.610.15271410.13726596X-RAY DIFFRACTION100
3.61-4.550.14451400.12496582X-RAY DIFFRACTION100
4.55-32.880.18141420.15326621X-RAY DIFFRACTION99.63
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)
11.67815965286-0.1949532836120.4797170177131.51123938866-0.01334003259322.867913416270.134259171790.205434683763-0.0502000616957-0.0234521993535-0.1421693879380.1212264331510.237480120779-0.291331001129-0.003523707332920.183999640023-0.0262978279085-0.03095971044180.347240193929-0.02593488536660.26524680997111.77736032-80.232004271612.5512193734
23.509515098642.02094721371.478075905994.400962095711.832681248695.062688204150.116174123451-0.02336408917050.00811336975251-0.00807941084214-0.0267923452007-0.1659881441-0.1255953352870.100543055597-0.07744990182350.1737060724720.0291966099620.02286680122620.2075005334170.02520946194530.24632731814532.3587822407-68.65727036223.8464644359
31.742371641190.236009261886-0.04481331646391.865057651260.5027180219652.687557768650.0445770943474-0.005550927568220.05042577785520.291375456931-0.02155879547470.0111488493509-0.1272839761790.189166781344-0.02333337752560.311904595655-0.0774932286578-0.01106798272560.185852641184-0.01514568861550.25226298370858.3623831566-48.535116319617.6427839233
45.956570960341.370228154682.05698058862.088823001450.6900419864994.68934352879-0.04253533208340.110665078302-0.1572636065040.03477229633580.1140716601930.04826360488480.0387893387526-0.113089616948-0.04846162045290.2493984678080.0009382089055560.03861036783080.1813802264930.001144477840760.26336515375439.9901435712-63.77514365976.47821475875
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11((chain 'A' and resid 1 through 11) and (chain 'B' and resid 16 through 146) and (chain 'C' and resid 149 through 245))A - CA - C1 - 2451 - 245
22(chain 'D' and resid 1 through 58)BB1 - 581 - 58
31((chain 'E' and resid 1 through 11) and (chain 'F' and resid 16 through 146) and (chain 'G' and resid 149 through 245))E - GE - G1 - 2451 - 245
44(chain 'H' and resid 1 through 58)HH1 - 581 - 58

+
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