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- PDB-1a0l: HUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACIN... -

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Basic information

Entry
Database: PDB / ID: 1a0l
TitleHUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACING A CENTRAL PORE
ComponentsBETA-TRYPTASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN-LIKE SERINE PROTEINASE / TETRAMER / HEPARIN / ALLERGY / ASTHMA / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
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-APA / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPereira, P.J.B. / Bergner, A. / Macedo-Ribeiro, S. / Huber, R. / Matschiner, G. / Fritz, H. / Sommerhoff, C.P. / Bode, W.
CitationJournal: Nature / Year: 1998
Title: Human beta-tryptase is a ring-like tetramer with active sites facing a central pore.
Authors: Pereira, P.J. / Bergner, A. / Macedo-Ribeiro, S. / Huber, R. / Matschiner, G. / Fritz, H. / Sommerhoff, C.P. / Bode, W.
History
DepositionDec 3, 1997Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-TRYPTASE
B: BETA-TRYPTASE
C: BETA-TRYPTASE
D: BETA-TRYPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4108
Polymers109,5774
Non-polymers8334
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-33 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 82.930, 172.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.960332, 0.276891, -0.033061), (0.275832, 0.925793, -0.258505), (-0.04097, -0.25737, -0.965444)132.62109, 5.2743, 181.90961
2given(-0.999796, -0.001683, 0.020114), (0.007034, -0.9631, 0.269053), (0.018919, 0.269139, 0.962915)140.32651, 43.3124, -7.408
3given(0.961787, -0.270732, 0.040859), (-0.270396, -0.962653, -0.013641), (0.043026, 0.002071, -0.999072)8.4737, 87.6665, 170.3678

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Components

#1: Protein
BETA-TRYPTASE


Mass: 27394.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: IN COMPLEX WITH AMIDINO PHENYL PYRUVIC ACID (APPA), A SYNTHETIC INHIBITOR
Source: (natural) Homo sapiens (human) / Cell: MAST CELL / Organ: LUNG / References: UniProt: P20231, tryptase
#2: Chemical
ChemComp-APA / (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid


Mass: 208.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFOR ALL FOUR CHAINS, THE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA IS COVALENTLY CONNECTED TO THE ...FOR ALL FOUR CHAINS, THE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA IS COVALENTLY CONNECTED TO THE CORRESPONDING SER195 SIDE CHAIN ATOM OG, FORMING HEMIKETAL.

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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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Msodium chloride1drop
23 Mammonium sulfate1reservoir
30.2 M3-(N-morpholino)propanesulphonic acid1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.121
Reflection
*PLUS
Num. obs: 23164

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→10 Å / Data cutoff high absF: 10000000000 / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 -5 %RANDOM
Rwork0.197 ---
obs0.197 22536 99.3 %-
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 60 96 7872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.004
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.69
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.434
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.449 -5.7 %
Rwork0.316 2089 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.69
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.434
LS refinement shell
*PLUS
Rfactor obs: 0.316

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