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- PDB-2fxr: human beta tryptase II complexed with activated ketone inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 2fxr
Titlehuman beta tryptase II complexed with activated ketone inhibitor CRA-29382
ComponentsTryptase beta-2
KeywordsHYDROLASE / serine protease / activated ketone inhibitor / pyrrolidine / CRA-29382
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / : / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
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 ...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
Chem-C3A / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKatz, B.A.
CitationJournal: Biochemistry / Year: 2006
Title: Structure-guided design of Peptide-based tryptase inhibitors.
Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / ...Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / Green, M.J. / Lee, C.-S. / Liu, L. / Tai, V. / Spencer, J. / Sperandio, D. / Katz, B.A.
History
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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: Tryptase beta-2
B: Tryptase beta-2
C: Tryptase beta-2
D: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1968
Polymers109,9664
Non-polymers2,2314
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-63 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.202, 78.202, 165.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological unit is the tetramer. Each asymmetric unit contains one biologically-relevant tetramer.

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Components

#1: Protein
Tryptase beta-2 / Tryptase-2 / Tryptase II


Mass: 27491.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPSB2, TPS2 / Production host: Pichia pastoris (fungus) / References: UniProt: P20231, tryptase
#2: Chemical
ChemComp-C3A / ALLYL {(1S)-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]-3-PYRROLIDIN-3-YLPROPYL}CARBAMATE


Mass: 557.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H35N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2mg/mL protein, 10 mM MES, pH 6.1, 2M NaCl dissolved in 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution ...Details: 2mg/mL protein, 10 mM MES, pH 6.1, 2M NaCl dissolved in 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ratios of protein solution to crystallization solution. Crystals appropriate for diffraction studies appeared in 2-5 days at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→42.78 Å / Num. all: 39151 / Num. obs: 39151 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.101
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.557 / % possible all: 98.5

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Processing

Software
NameClassification
HKL-2000data reduction
EPMRphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0L

1a0l


Resolution: 2.5→42.78 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3659 -RANDOM
Rwork0.22 ---
obs0.223 36299 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7677 0 164 82 7923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.007
X-RAY DIFFRACTIONc_bond_d1.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2cra.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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