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- PDB-2fww: human beta-tryptase II complexed with 4-piperidinebutyrate to mak... -

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Basic information

Entry
Database: PDB / ID: 2fww
Titlehuman beta-tryptase II complexed with 4-piperidinebutyrate to make acylenzyme
ComponentsTryptase beta-2
KeywordsHYDROLASE / serine protease / proteinase / 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
4-PIPERIDINEBUTYRATE / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 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 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 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 / Item: _software.classification / _software.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)110,5878
Polymers109,9664
Non-polymers6214
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-3 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.92, 77.92, 164.03
Angle α, β, γ (deg.)90.0, 90.0, 120.0
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-C1R / 4-PIPERIDINEBUTYRATE / 4-PIPERIDIN-4-YLBUTANAL


Mass: 155.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K
Details: 2mg/mL of protein, 10 mM MES, pH 6.1, 2M NaCl was mixed with crystallization solution 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using ...Details: 2mg/mL of protein, 10 mM MES, pH 6.1, 2M NaCl was mixed with crystallization solution 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: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 52849 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.25→2.29 Å / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 5035 10 %RANDOM
Rwork0.212 ---
obs0.212 49762 94.1 %-
all-52849 --
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7677 0 44 611 8332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 546 10 %
Rwork0.293 5030 -
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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