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- PDB-5xx4: A BPTI-[5,55] variant with C14GA38K mutations -

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Basic information

Entry
Database: PDB / ID: 5xx4
TitleA BPTI-[5,55] variant with C14GA38K mutations
ComponentsPancreatic trypsin inhibitor
KeywordsHYDROLASE / HYDROLASE 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 ...: / 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 / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsIslam, M.M.
CitationJournal: Febs J. / Year: 2019
Title: Hydrophobic surface residues can stabilize a protein through improved water-protein interactions.
Authors: Islam, M.M. / Kobayashi, K. / Kidokoro, S.I. / Kuroda, Y.
History
DepositionJul 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)13,2356
Polymers12,8512
Non-polymers3844
Water4,161231
1
A: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7144
Polymers6,4251
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-24 kcal/mol
Surface area4010 Å2
MethodPISA
2
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5212
Polymers6,4251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-16 kcal/mol
Surface area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.201, 41.171, 54.742
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6425.345 Da / Num. of mol.: 2 / Mutation: A14G, A38K
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCL, pH8.5

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Data collection

DiffractionMean temperature: 101.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→53.84 Å / Num. obs: 12943 / % possible obs: 99.4 % / Redundancy: 3.6 % / Net I/σ(I): 4.23
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.87 / Rsym value: 0.223 / % possible all: 95.9

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Processing

Software
NameVersionClassification
SHELXL5.8.0049data collection
DENZOdata reduction
SCALAdata scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZVX

2zvx


Resolution: 1.67→53.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.531 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22039 627 4.9 %RANDOM
Rwork0.14197 ---
obs0.14566 12243 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20.35 Å2
2---0.57 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.67→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 20 231 1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019927
X-RAY DIFFRACTIONr_bond_other_d0.0010.02844
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.981252
X-RAY DIFFRACTIONr_angle_other_deg0.98631927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.09921.16343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021511
X-RAY DIFFRACTIONr_chiral_restr0.1230.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9861.063462
X-RAY DIFFRACTIONr_mcbond_other1.9981.057461
X-RAY DIFFRACTIONr_mcangle_it2.2551.584574
X-RAY DIFFRACTIONr_mcangle_other2.2581.591575
X-RAY DIFFRACTIONr_scbond_it2.5721.375465
X-RAY DIFFRACTIONr_scbond_other2.5311.357458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5021.905667
X-RAY DIFFRACTIONr_long_range_B_refined4.3611.9581241
X-RAY DIFFRACTIONr_long_range_B_other3.52110.1481096
X-RAY DIFFRACTIONr_rigid_bond_restr5.78131771
X-RAY DIFFRACTIONr_sphericity_free23.377543
X-RAY DIFFRACTIONr_sphericity_bonded9.01651939
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 45 -
Rwork0.148 867 -
obs--95.2 %

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