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- PDB-5xx2: A BPTI-[5,55] variant with C14GA38L mutations -

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Basic information

Entry
Database: PDB / ID: 5xx2
TitleA BPTI-[5,55] variant with C14GA38L 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 1.3Nov 6, 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)13,3958
Polymers12,8192
Non-polymers5766
Water6,287349
1
A: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7945
Polymers6,4091
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area4010 Å2
MethodPISA
2
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6013
Polymers6,4091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.413, 40.690, 61.147
Angle α, β, γ (deg.)90.00, 89.99, 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: 6409.323 Da / Num. of mol.: 2 / Mutation: A14G, A38L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
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 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→61.15 Å / Num. obs: 67481 / % possible obs: 99.5 % / Redundancy: 6.4 % / Net I/σ(I): 6.32
Reflection shellResolution: 1→1.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 6.32 / Rsym value: 0.289 / % possible all: 99.9

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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: 1.12→61.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.537 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14575 3274 5.1 %RANDOM
Rwork0.13048 ---
obs0.13126 61177 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.14 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.12→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 30 360 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.019968
X-RAY DIFFRACTIONr_bond_other_d0.0040.02904
X-RAY DIFFRACTIONr_angle_refined_deg2.9881.9961308
X-RAY DIFFRACTIONr_angle_other_deg0.99532066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.18220.43546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.52815150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7171514
X-RAY DIFFRACTIONr_chiral_restr0.1850.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
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_it0.680.483466
X-RAY DIFFRACTIONr_mcbond_other0.6830.482465
X-RAY DIFFRACTIONr_mcangle_it0.7880.733580
X-RAY DIFFRACTIONr_mcangle_other0.7880.734581
X-RAY DIFFRACTIONr_scbond_it1.7650.63502
X-RAY DIFFRACTIONr_scbond_other1.7640.631503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5760.894727
X-RAY DIFFRACTIONr_long_range_B_refined4.1577.7621504
X-RAY DIFFRACTIONr_long_range_B_other2.5135.1471196
X-RAY DIFFRACTIONr_rigid_bond_restr6.84331872
X-RAY DIFFRACTIONr_sphericity_free35.759528
X-RAY DIFFRACTIONr_sphericity_bonded11.54752184
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 242 -
Rwork0.196 4333 -
obs--91.79 %

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