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- PDB-5xx8: Hetero-micro-seeding: Crystal structure of BPTI-[555]C14GA38I var... -

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Basic information

Entry
Database: PDB / ID: 5xx8
TitleHetero-micro-seeding: Crystal structure of BPTI-[555]C14GA38I variant using micro-seeds from -C14GA38L variant
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: 1.3 Å
AuthorsIslam, M.M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: A hetero-micro-seeding strategy for readily crystallizing closely related protein variants
Authors: Islam, M.M. / Kuroda, Y.
History
DepositionJul 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,0114
Polymers12,8192
Non-polymers1922
Water5,567309
1
A: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5052
Polymers6,4091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area4240 Å2
MethodPISA
2
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5052
Polymers6,4091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.279, 41.479, 53.971
Angle α, β, γ (deg.)90.00, 99.35, 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, A38I
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20-30%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-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: 1.3→53.25 Å / Num. obs: 27383 / % possible obs: 96.9 % / Redundancy: 3.6 % / Net I/σ(I): 4.23
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.23 / Rsym value: 0.28 / % possible all: 98.8

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Processing

Software
NameVersionClassification
SHELXL5.8.0158data collection
DENZOdata reduction
SCALAdata scaling
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZVX

2zvx


Resolution: 1.3→53.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.799 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20647 1446 5.5 %RANDOM
Rwork0.1623 ---
obs0.16471 25022 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.408 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→53.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 10 310 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.019939
X-RAY DIFFRACTIONr_bond_other_d0.0030.02869
X-RAY DIFFRACTIONr_angle_refined_deg2.4241.9741266
X-RAY DIFFRACTIONr_angle_other_deg1.32232005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.27321.36444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1741511
X-RAY DIFFRACTIONr_chiral_restr0.2360.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
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_it1.1370.848464
X-RAY DIFFRACTIONr_mcbond_other1.1030.845463
X-RAY DIFFRACTIONr_mcangle_it1.6811.27577
X-RAY DIFFRACTIONr_mcangle_other1.6871.272578
X-RAY DIFFRACTIONr_scbond_it2.1291.112475
X-RAY DIFFRACTIONr_scbond_other2.1221.102468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1121.545677
X-RAY DIFFRACTIONr_long_range_B_refined5.38714.1041246
X-RAY DIFFRACTIONr_long_range_B_other4.7911.4571085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 91 -
Rwork0.211 1855 -
obs--95.21 %

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