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- PDB-7qis: CRYSTAL STRUCTURE OF THE P1 difluoroethylglycine (DfeGly) BPTI MU... -

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Basic information

Entry
Database: PDB / ID: 7qis
TitleCRYSTAL STRUCTURE OF THE P1 difluoroethylglycine (DfeGly) 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: 1.83 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)67,67652
Polymers63,5648
Non-polymers4,11244
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28630 Å2
ΔGint-348 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.269, 100.269, 206.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain 'A' and resid 1 through 13) and (chain 'B'...
21(chain 'E' and resid 1 through 13) and (chain 'F'...
12(chain D and (resid 1 through 10 or resid 12...
22(chain G and (resid 1 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSLEULEUAA1 - 101 - 10
121ILEILEVALVALBB16 - 171 - 2
131GLYGLYASNASNBB19 - 484 - 33
141ASNASNASPASPBB50 - 6435 - 49
151VALVALGLYGLYBB66 - 7451 - 59
161SERSERSERSERBB76 - 7761 - 62
171ILEILEGLNGLNBB80 - 8165 - 66
181LEULEUSERSERBB83 - 9268 - 77
191TYRTYRASNASNBB94 - 9579 - 80
1101LEULEUTHRTHRBB97 - 9882 - 83
1111ASNASNPROPROBB100 - 12485 - 109
1121ALAALAASPASPBB126 - 128111 - 113
1131PHEPHETYRTYRBB130 - 146115 - 131
1141ALAALAASPASPCC149 - 1531 - 5
1151LEULEUASNASNCC155 - 1657 - 17
1161CYSCYSCYSCYSCC168 - 19120 - 43
1171GLYGLYCYSCYSCC193 - 20145 - 53
1181TRPTRPSERSERCC207 - 21759 - 69
1191THRTHRSERSERCC219 - 22371 - 75
1201PROPROVALVALCC225 - 22777 - 79
1211ALAALAASNASNCC229 - 24581 - 97
211CYSCYSLEULEUEE1 - 101 - 10
221ILEILEVALVALFF16 - 171 - 2
231GLYGLYASNASNFF19 - 484 - 33
241ASNASNASPASPFF50 - 6435 - 49
251VALVALGLYGLYFF66 - 7451 - 59
261SERSERSERSERFF76 - 7761 - 62
271ILEILEGLNGLNFF80 - 8165 - 66
281LEULEUSERSERFF83 - 9268 - 77
291TYRTYRASNASNFF94 - 9579 - 80
2101LEULEUTHRTHRFF97 - 9882 - 83
2111ASNASNPROPROFF100 - 12485 - 109
2121ALAALAASPASPFF126 - 128111 - 113
2131PHEPHETYRTYRFF130 - 146115 - 131
2141ALAALAASPASPGG149 - 1531 - 5
2151LEULEUASNASNGG155 - 1657 - 17
2161CYSCYSCYSCYSGG168 - 19120 - 43
2171GLYGLYCYSCYSGG193 - 20145 - 53
2181TRPTRPSERSERGG207 - 21759 - 69
2191THRTHRSERSERGG219 - 22371 - 75
2201PROPROVALVALGG225 - 22777 - 79
2211ALAALAASNASNGG229 - 24581 - 97
112ARGARGTYRTYRDD1 - 101 - 10
122GLYGLYALAALADD12 - 1612 - 16
132ILEILECYSCYSDD18 - 3018 - 30
142THRTHRALAALADD32 - 5832 - 58
212ARGARGTYRTYRHH1 - 101 - 10
222GLYGLYALAALAHH12 - 1612 - 16
232ILEILECYSCYSHH18 - 3018 - 30
242THRTHRALAALAHH32 - 5832 - 58

NCS ensembles :
ID
1
2

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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: 6519.474 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, 647 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.: 603 / 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: 1.83→50 Å / Num. obs: 103236 / % possible obs: 99.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 35.1 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.209 / Net I/σ(I): 10.57
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 0.96 / Num. unique obs: 16710 / CC1/2: 0.527 / Rrim(I) all: 3.069 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8N

1t8n


Resolution: 1.83→32.82 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 2095 2.03 %
Rwork0.1627 100895 -
obs0.1633 102990 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.72 Å2 / Biso mean: 36.8813 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 1.83→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 249 603 5276
Biso mean--57.85 45.25 -
Num. residues----596
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1776X-RAY DIFFRACTION3.478TORSIONAL
12C1776X-RAY DIFFRACTION3.478TORSIONAL
21B504X-RAY DIFFRACTION3.478TORSIONAL
22D504X-RAY DIFFRACTION3.478TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.870.43241390.35756686682599
1.87-1.920.32091390.302866966835100
1.92-1.970.31181390.259467096848100
1.97-2.030.2381400.236867036843100
2.03-2.090.26051400.22567506890100
2.09-2.170.26181390.204566946833100
2.17-2.250.23231380.187466946832100
2.25-2.360.21061400.17167296869100
2.36-2.480.21091400.164367526892100
2.48-2.640.18341410.157867656906100
2.64-2.840.17971380.156466866824100
2.84-3.130.20941410.152767676908100
3.13-3.580.15421400.138767596899100
3.58-4.510.1281400.117967376877100
4.51-32.820.15841410.145567686909100
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)
11.3628-0.27720.04481.52510.33971.99730.04080.0129-0.0382-0.2586-0.03450.01810.09520.1824-0.00460.29630.0720.00910.1717-0.01530.2328.1875-38.43030.8011
20.33160.015-0.10450.409-0.14090.2673-0.0321-0.12290.05360.00180.09540.05420.13210.00770.00010.23150.0109-0.0320.2252-0.01170.2546-10.0447-23.41111.6947
31.53330.1172-0.27961.04050.04092.28960.1109-0.19730.03020.0157-0.13520.0695-0.1799-0.2697-0.00180.16090.01770.02960.3265-0.02450.2401-38.5068-6.5395.9536
40.42480.1420.07640.40740.19450.31130.09950.0277-0.0222-0.0247-0.0181-0.08190.0865-0.09540.00010.23260.0089-0.00540.2630.01920.2733-17.7954-18.3458-5.6088
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 12) 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 12) 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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