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- PDB-7qiq: CRYSTAL STRUCTURE OF THE P1 aminobutanoic acid (ABU) BPTI MUTANT-... -

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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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / Peptidase S1A, chymotrypsin family ...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 / 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 / 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 (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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 (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 (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 (cattle) / References: UniProt: P00766

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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 (cattle) / References: UniProt: P00974

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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

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Details

Has ligand of interestY

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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

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).

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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

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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

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