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- PDB-2fpz: Human tryptase with 2-amino benzimidazole -

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Basic information

Entry
Database: PDB / ID: 2fpz
TitleHuman tryptase with 2-amino benzimidazole
ComponentsTryptase beta-2
KeywordsHYDROLASE / Serine protease / drug design
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
2H-BENZOIMIDAZOL-2-YLAMINE / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSomoza, J.R.
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
DepositionJan 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)110,4988
Polymers109,9664
Non-polymers5334
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-15 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.895, 78.895, 165.981
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a tetramer. This is the same tetramer that forms the asymmetric unit.

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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-270 / 2H-BENZOIMIDAZOL-2-YLAMINE / ZK-800270


Mass: 133.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 4.6
Details: 0.1M sodium acetate, 0.2M ammonium sulfate, 30% PEG 1500, pH 4.6, VAPOR DIFFUSION, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 76856 / Num. obs: 76856 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.97 Å / FOM work R set: 0.837 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 7144 9.2 %Random
Rwork0.207 ---
obs0.21 70965 90.9 %-
all-70965 --
Displacement parametersBiso mean: 23.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.874 Å2-1.976 Å20 Å2
2---0.874 Å20 Å2
3---1.748 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 40 520 8240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.010.3091020.2899941096
2.01-2.030.3081440.2611601304
2.03-2.040.3151290.25911651294
2.04-2.060.2981100.25211261236
2.06-2.070.3171280.25812691397
2.07-2.090.2851450.24811751320
2.09-2.10.2551390.23311611300
2.1-2.120.2731190.23512341353
2.12-2.140.2491350.23312511386
2.14-2.150.2991370.2411841321
2.15-2.170.261520.21312401392
2.17-2.190.2811520.22712541406
2.19-2.210.2771400.23611281268
2.21-2.230.3531250.2689541079
2.23-2.250.3371270.27812771404
2.25-2.270.3241430.31713721515
2.27-2.30.2791030.2479881091
2.3-2.320.2631500.22512001350
2.32-2.350.2251200.2212501370
2.35-2.370.2371580.19213271485
2.37-2.40.2481240.20713221446
2.4-2.430.2921460.20813181464
2.43-2.460.2431550.19313041459
2.46-2.490.261460.21613461492
2.49-2.520.2671530.21113061459
2.52-2.550.2941560.22813521508
2.55-2.590.2711420.21212931435
2.59-2.630.231410.2113991540
2.63-2.670.2651460.22312941440
2.67-2.710.3081500.23413651515
2.71-2.760.2991490.22513121461
2.76-2.810.251500.23213721522
2.81-2.870.2741470.22413531500
2.87-2.920.2871740.23613051479
2.92-2.990.2811650.24513541519
2.99-3.060.2871600.24713801540
3.06-3.130.2641380.23713901528
3.13-3.220.2531540.21613441498
3.22-3.310.2421600.2214001560
3.31-3.420.2221540.19714021556
3.42-3.540.211640.18513451509
3.54-3.680.2181010.2069871088
3.68-3.850.2071330.18311591292
3.85-4.050.2131550.1713641519
4.05-4.310.1781390.15414171556
4.31-4.640.1651610.1414181579
4.64-5.110.1491620.14113791541
5.11-5.850.2061630.18213701533
5.85-7.360.2021530.18314161569
7.36-500.1711450.16113461491
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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