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- PDB-1qlq: Bovine Pancreatic Trypsin Inhibitor (BPTI) Mutant with Altered Bi... -

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Basic information

Entry
Database: PDB / ID: 1qlq
TitleBovine Pancreatic Trypsin Inhibitor (BPTI) Mutant with Altered Binding Loop Sequence
ComponentsPANCREATIC TRYPSIN INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsCzapinska, H. / Krzywda, S. / Sheldrick, G.M. / Otlewski, J. / Jaskolski, M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: High Resolution Structure of Bovine Pancreatic Trypsin Inhibitor with Altered Binding Loop Sequence
Authors: Czapinska, H. / Otlewski, J. / Krzywda, S. / Sheldrick, G.M. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of Bovine Pancreatic Trypsin Inhibitor at 125 K: Definition of Carboxyl-Terminal Residues Gly57 and Ala58
Authors: Parkin, S. / Rupp, B. / Hope, H.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of a High Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures
Authors: Berndt, K. / Guentert, P. / Orbons, L.P. / Wuethrich, K.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Bovine Pancreatic Trypsin Inhibitor . Results of Joint Neutron and X-Ray Refinement of Crystal Form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1975
Title: Crystallographic Refinement of the Structure of Bovine Pancreatic Trypsin Inhibitor at 1.5 A Resolution
Authors: Deisenhofer, J. / Steigemann, W.
History
DepositionSep 10, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8665
Polymers6,4811
Non-polymers3844
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.710, 52.710, 43.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-64-

SO4

21A-2079-

HOH

DetailsTHE ASYMMETRIC UNIT CONTAINS THE MONOMERIC MOLECULE.AN EXTRA WATER MOLECULE IS BURIED IN AN INTERNAL CLEFT.IN THE CRYSTAL THE ARG17-ILE18- ILE19 SEGMENTS OF THE PROTEINMOLECULES RELATED BY THE (Y, X, -Z) TWO-FOLD ROTATION FORMAN INTERMOLECULAR ANTIPARALLEL B-SHEET.A DIFFERENT INTERMOLECULAR ANTIPARALLEL B-SHEET IS FOUNDIN THE CRYSTAL FOR THE BPTI 8PTI WHERE IN SPACE GROUPP 42 21 2, STRAND 31 TO 35 IS INVOLVED IN A CRYSTAL PACKINGDIMER. FOR THE BPTI STRUCTURES 6PTI AND 1NAG THE LOOP39 TO 42 IS INVOLVED IN A DIFFERENT TIGHT CRYSTALPACKING, SPACE GROUP P 21 21 2, WHILE A DECAMER IS OBSERVEDFOR THE BPTI IN ENTRIES 1B0C AND 1BZ5.

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Components

#1: Protein PANCREATIC TRYPSIN INHIBITOR / BPTI / APROTININ / TRASYLOL / BASIC PROTEASE INHIBITOR


Mass: 6481.481 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: PANCREAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T7 / References: UniProt: P00974
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/ML. 2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH ...Details: A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/ML. 2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 2% PEG 400, 2 M AMMONIUM SULFATE AND 0.1 M NA HEPES, PH 7.5. THE HANGING DROPLETS WERE EQUILIBRATED AT 19 DEG C THROUGH THE GAS PHASE WITH THE RESERVOIR. PRISMATIC CRYSTALS MEASURING UP TO 0.4 MM GREW WITHIN 12 HOURS.
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
22 %PEG4001reservoir
32.0 Mammonium sulfate1reservoir
40.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS SRA2 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.42→20 Å / Num. obs: 11934 / % possible obs: 99.6 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 50.2
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 6 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 5.144 / % possible all: 96
Reflection shell
*PLUS
% possible obs: 96 % / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPI

1bpi


Resolution: 1.42→10 Å / Num. parameters: 5297 / Num. restraintsaints: 5730 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N- TERMINUS. THE CYS14-CYS38 DISULFIDE BRIDGE IS OBSERVED IN TWO DISTINCT CHIRALITIES (63 % RIGHT- ...Details: ANISOTROPIC REFINEMENT. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N- TERMINUS. THE CYS14-CYS38 DISULFIDE BRIDGE IS OBSERVED IN TWO DISTINCT CHIRALITIES (63 % RIGHT-HANDED, 37 % LEFT-HANDED). ONE TWO-FOLD SYMMETRIC AND THREE GENERAL-POSITION SULFATE ANIONS ARE PRESENT PER ONE PROTEIN MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 1009 8.5 %RANDOM
all0.1103 11846 --
obs0.1087 -99.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 429 / Occupancy sum non hydrogen: 544.5
Refinement stepCycle: LAST / Resolution: 1.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 18 98 568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0278
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1087 / Rfactor obs: 0.1048
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.072

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