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- PDB-2gdd: Human beta II tryptase with inhibitor CRA-27592 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2gdd
TitleHuman beta II tryptase with inhibitor CRA-27592
ComponentsTryptase beta-2
KeywordsHYDROLASE / Serine protease
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-5AM / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Human beta II tryptase with inhibitor CRA-27592
Authors: Somoza, J.R.
History
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 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)112,2818
Polymers109,9664
Non-polymers2,3154
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-70 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.015, 78.015, 163.98
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number144
Space group name H-MP31
DetailsThe asymmetric unit is a tetramer, which is the biological 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-5AM / BENZYL {(1S)-5-AMINO-1-[(S)-HYDROXY(5-{[4-(4-PHENYLBUTANOYL)PIPERAZIN-1-YL]METHYL}-1,2,4-OXADIAZOL-3-YL)METHYL]PENTYL}CARBAMATE


Mass: 578.702 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H42N6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: Tryptase was purchased from Promega (catalog #G563X). The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc ...Details: Tryptase was purchased from Promega (catalog #G563X). The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500 (all reagents obtained from Hampton Research). Crystallization drops were set up at various ratios of protein solution to crystallization solution. Crystals appeared in 2-5 days at room temperature., VAPOR DIFFUSION, 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: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→19.7 Å / Num. obs: 46451 / % possible obs: 100 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.138 / Χ2: 1.078 / Net I/σ(I): 6.6
Reflection shellResolution: 2.35→2.39 Å / % possible obs: 100 % / Rmerge(I) obs: 0.757 / Num. unique obs: 2309 / Χ2: 0.912 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.7 Å / FOM work R set: 0.814 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4369 9.4 %RANDOM
Rwork0.215 ---
obs0.219 43417 93.4 %-
Displacement parametersBiso mean: 28.072 Å2
Baniso -1Baniso -2Baniso -3
1--3.296 Å2-4.88 Å20 Å2
2---3.296 Å20 Å2
3---6.593 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 168 136 7984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
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
2.35-2.370.346790.296701780
2.37-2.380.289940.291688782
2.38-2.40.38740.298707781
2.4-2.420.327860.291748834
2.42-2.430.363790.29696775
2.43-2.450.31880.296722810
2.45-2.470.341800.276697777
2.47-2.490.323960.273756852
2.49-2.510.317750.278756831
2.51-2.530.314720.287731803
2.53-2.550.368890.271735824
2.55-2.580.359750.276692767
2.58-2.60.287790.267771850
2.6-2.620.331810.275730811
2.62-2.650.337850.289758843
2.65-2.670.254880.254744832
2.67-2.70.289810.267788869
2.7-2.730.303740.25762836
2.73-2.760.314740.271784858
2.76-2.790.349880.261763851
2.79-2.820.294880.283780868
2.82-2.850.343870.268760847
2.85-2.890.338900.278819909
2.89-2.920.304900.239746836
2.92-2.960.284850.258807892
2.96-30.273970.249821918
3-3.040.347790.25740819
3.04-3.090.253990.251804903
3.09-3.140.291950.241841936
3.14-3.190.308880.255770858
3.19-3.240.27990.239817916
3.24-3.30.242900.232818908
3.3-3.370.258970.227823920
3.37-3.440.255840.207820904
3.44-3.510.238910.2805896
3.51-3.590.24890.2798887
3.59-3.680.251070.218838945
3.68-3.780.231090.183797906
3.78-3.890.23950.203832927
3.89-4.020.228840.185820904
4.02-4.160.167860.146816902
4.16-4.330.222920.151881973
4.33-4.520.19810.154813894
4.52-4.760.204870.159807894
4.76-5.060.164980.148832930
5.06-5.450.202790.183854933
5.45-60.184930.193839932
6-6.870.2041000.19814914
6.87-8.640.1931050.161830935
8.64-500.208680.148777845
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2inh2.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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