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- PDB-2fs8: Human beta-tryptase II with inhibitor CRA-29382 -

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Basic information

Entry
Database: PDB / ID: 2fs8
TitleHuman beta-tryptase II with inhibitor CRA-29382
ComponentsTryptase beta-2
KeywordsHYDROLASE / Serine protease / proteinase / 29382
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
Chem-C3A / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-62 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.202, 78.202, 165.516
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-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 / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2mg/mL protein in 10mM MES, pH 6.1, 2M NaCl mixed in reservoir solution containing 0.1 M NaOAc, pH 4.6, 0.2 M ammonium sulfate, 30% PEG 1500. Crystallization drops were set up using various ...Details: 2mg/mL protein in 10mM MES, pH 6.1, 2M NaCl mixed in reservoir solution containing 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: 100 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(I): -3 / Rmerge(I) obs: 0.101 / Χ2: 0.931
Reflection shellResolution: 2.5→2.54 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.557 / Num. unique obs: 1927 / Χ2: 0.801 / % possible all: 98.5

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Phasing

Phasing MRRfactor: 0.317 / Cor.coef. Fo:Fc: 0.743
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.2phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.78 Å / FOM work R set: 0.81 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3659 9.3 %RANDOM
Rwork0.205 ---
obs0.21 36299 92.7 %-
Displacement parametersBiso mean: 29.365 Å2
Baniso -1Baniso -2Baniso -3
1--3.942 Å2-6.282 Å20 Å2
2---3.942 Å20 Å2
3---7.883 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 164 196 8040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
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
2.5-2.520.437700.342556626
2.52-2.530.371610.376550611
2.53-2.550.359670.291580647
2.55-2.570.394610.34571632
2.57-2.590.296610.299641702
2.59-2.610.318720.292610682
2.61-2.630.405610.286561622
2.63-2.650.332720.28654726
2.65-2.670.328720.267602674
2.67-2.690.27630.261630693
2.69-2.720.357640.301590654
2.72-2.740.338770.253637714
2.74-2.760.272650.241642707
2.76-2.790.292800.283646726
2.79-2.820.492630.292643706
2.82-2.840.349690.277617686
2.84-2.870.283660.285626692
2.87-2.90.374810.289653734
2.9-2.930.331740.282601675
2.93-2.960.311590.264647706
2.96-30.303720.274666738
3-3.030.357720.275630702
3.03-3.070.336770.245660737
3.07-3.110.326680.259668736
3.11-3.150.313850.252671756
3.15-3.190.292840.235618702
3.19-3.240.273700.234719789
3.24-3.290.3760.223638714
3.29-3.340.291840.225679763
3.34-3.390.298600.21715775
3.39-3.450.196790.189657736
3.45-3.510.278750.2664739
3.51-3.580.252720.223678750
3.58-3.650.257770.198684761
3.65-3.730.231750.191707782
3.73-3.820.244650.174669734
3.82-3.920.232600.188712772
3.92-4.020.186830.154661744
4.02-4.140.168870.152694781
4.14-4.270.183730.135675748
4.27-4.430.158890.135667756
4.43-4.60.168810.148728809
4.6-4.810.185800.143680760
4.81-5.070.173840.133691775
5.07-5.380.224670.152685752
5.38-5.80.212800.176685765
5.8-6.380.243860.189689775
6.38-7.30.186870.159688775
7.3-9.190.165850.137692777
9.19-500.194680.164713781
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2cra2.par
X-RAY DIFFRACTION3water_rep.param

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