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- PDB-2uux: Structure of the tryptase inhibitor TdPI from a tick -

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Basic information

Entry
Database: PDB / ID: 2uux
TitleStructure of the tryptase inhibitor TdPI from a tick
ComponentsTRYPTASE INHIBITOR
KeywordsINHIBITOR / TRYPTASE INHIBITOR
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Pancreatic trypsin inhibitor Kunitz domain superfamily / serine-type endopeptidase inhibitor activity / Few Secondary Structures / Irregular / Tryptase inhibitor
Function and homology information
Biological speciesRHIPICEPHALUS APPENDICULATUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsSiebold, C. / Paesen, G.C. / Harlos, K. / Peacey, M.F. / Nuttall, P.A. / Stuart, D.I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Tick Protein with a Modified Kunitz Fold Inhibits Human Tryptase.
Authors: Paesen, G.C. / Siebold, C. / Harlos, K. / Peacey, M.F. / Nuttall, P.A. / Stuart, D.I.
History
DepositionMar 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2413
Polymers6,0491
Non-polymers1922
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.676, 28.594, 30.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRYPTASE INHIBITOR / TRYPTASE INHIBITOR TDPI


Mass: 6049.021 Da / Num. of mol.: 1 / Fragment: RESIDUES 44-96 / Source method: isolated from a natural source / Source: (natural) RHIPICEPHALUS APPENDICULATUS (arthropod) / References: UniProt: Q1EG59
#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.: 78 / 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

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Sample preparation

CrystalDensity Matthews: 1.58 Å3/Da / Density % sol: 35.56 %
Crystal growDetails: 2.4 M AMMONIUM SULFATE 0.1 M TRIS-HCL, PH 8 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 10942 / % possible obs: 91 % / Observed criterion σ(I): 1.5 / Redundancy: 8.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 72

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→19.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.504 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 451 5.1 %RANDOM
Rwork0.168 ---
obs0.171 8454 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms415 0 10 78 503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022457
X-RAY DIFFRACTIONr_bond_other_d0.0030.02328
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.973620
X-RAY DIFFRACTIONr_angle_other_deg0.9473.021776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28820.52619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7561572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.337155
X-RAY DIFFRACTIONr_chiral_restr0.0960.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02105
X-RAY DIFFRACTIONr_nbd_refined0.2320.271
X-RAY DIFFRACTIONr_nbd_other0.1970.2330
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2212
X-RAY DIFFRACTIONr_nbtor_other0.0820.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1241.5339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6112436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5683231
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8984.5184
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.226 30
Rwork0.185 508

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