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- PDB-2uuy: Structure of a tick tryptase inhibitor in complex with bovine trypsin -

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Basic information

Entry
Database: PDB / ID: 2uuy
TitleStructure of a tick tryptase inhibitor in complex with bovine trypsin
Components
  • CATIONIC TRYPSIN
  • TRYPTASE INHIBITOR
KeywordsHYDROLASE / CALCIUM / ZYMOGEN / PROTEASE / DIGESTION / METAL-BINDING / SERINE PROTEASE / TRYPTASE INHIBITOR
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Tryptase inhibitor
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
RHIPICEPHALUS APPENDICULATUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATIONIC TRYPSIN
B: TRYPTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1924
Polymers29,1162
Non-polymers762
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.949, 67.690, 69.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CATIONIC TRYPSIN / TRYPSIN FROM BOVINE PANCREAS / BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-243 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Tissue: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein TRYPTASE INHIBITOR / TRYPTASE INHIBITOR TDPI


Mass: 5791.777 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-96 / Source method: isolated from a natural source / Source: (natural) RHIPICEPHALUS APPENDICULATUS (arthropod) / References: UniProt: Q1EG59
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 1.48 Å3/Da / Density % sol: 36 %
Crystal growDetails: 0.1 M BIS-TRIS, PH 6.5 0.2 M MGCL2 25% PEG3350 (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. obs: 77853 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.15→1.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→48.34 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.075 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.163 3902 5 %RANDOM
Rwork0.13 ---
obs0.132 73793 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.15→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 2 510 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222210
X-RAY DIFFRACTIONr_bond_other_d0.0020.021503
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9523037
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0113703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81224.80577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.613156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_nbd_refined0.2060.2402
X-RAY DIFFRACTIONr_nbd_other0.190.21590
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21075
X-RAY DIFFRACTIONr_nbtor_other0.0910.21215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2620.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5011.51469
X-RAY DIFFRACTIONr_mcbond_other0.6531.5597
X-RAY DIFFRACTIONr_mcangle_it2.10622319
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7263875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6634.5693
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: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 250 -
Rwork0.269 4683 -
obs--85.33 %

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