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- PDB-2zvx: Structure of a BPTI-[5,55] variant containing Gly/Val at the 14/3... -

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Basic information

Entry
Database: PDB / ID: 2zvx
TitleStructure of a BPTI-[5,55] variant containing Gly/Val at the 14/38th positions
ComponentsPancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / protein folding / protein stabilization / protein design / Pharmaceutical / Protease inhibitor / Secreted / Serine protease inhibitor / Disulfide bond
Function / homology
Function and homology information


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 / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...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 / 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 / SYNCHROTRON / AB INITIO / Resolution: 1.09 Å
AuthorsIslam, M.M. / Sohya, S. / Noguchi, K. / Yohda, M. / Kuroda, Y.
CitationJournal: Proteins / Year: 2009
Title: Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations
Authors: Islam, M.M. / Sohya, S. / Noguchi, K. / Kidokoro, S. / Yohda, M. / Kuroda, Y.
History
DepositionNov 24, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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

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Assembly

Deposited unit
A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0795
Polymers12,7912
Non-polymers2883
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-43.6 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.962, 40.844, 54.829
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6395.296 Da / Num. of mol.: 2 / Mutation: C14G, C30A, C38V, C51A, M52L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATIVELY FOLDED BPTI VARIANT ENGINEREED FROM THE WILD TYPE BPTI. THIS BPTI HAS A SINGLE DISSULFIDE ...NATIVELY FOLDED BPTI VARIANT ENGINEREED FROM THE WILD TYPE BPTI. THIS BPTI HAS A SINGLE DISSULFIDE BOND BETWEEN RESIDUE 5 AND 55, THE OTHER CYSTEINES BEING MUTATED TO A, G OR V. ADDITIONALLY, M52 WAS MUTATED TO L FOR PURIFICATION PURPOSE. THIS BPTI SEQUENCE CONTAINS A TOTAL OF 5 MUTATIONS (C14G, C30A, C38V, M52L AND C51A) WITH RESPECT TO THE WILD-TYPE SEQUENCE.

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 0.2M Lithium chloride, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→53.91 Å / Num. obs: 35190 / % possible obs: 96 % / Redundancy: 7 % / Rmerge(I) obs: 0.042 / Rsym value: 0.052
Reflection shellHighest resolution: 1.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.042 / Num. unique all: 37057

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 2ZJX

2zjx


Resolution: 1.09→53.91 Å / Num. parameters: 8342 / Num. restraintsaints: 11036 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 1861 5.3 %RANDOM
obs0.1787 35190 90.9 %-
all-35190 --
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 985.5
Refinement stepCycle: LAST / Resolution: 1.09→53.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 15 126 1026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0297
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.07

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