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- PDB-5wi6: Human beta-1 tryptase mutant Ile99Cys -

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Open data


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Basic information

Entry
Database: PDB / ID: 5wi6
TitleHuman beta-1 tryptase mutant Ile99Cys
ComponentsTryptase alpha/beta-1
Keywordshydrolase/hydrolase inhibitor / disulfide mutation / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
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
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsEigenbrot, C. / Maun, H.R.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Dual functionality of beta-tryptase protomers as both proteases and cofactors in the active tetramer.
Authors: Maun, H.R. / Liu, P.S. / Franke, Y. / Eigenbrot, C. / Forrest, W.F. / Schwartz, L.B. / Lazarus, R.A.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 16, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.3Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
C: Tryptase alpha/beta-1
D: Tryptase alpha/beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,12115
Polymers109,8654
Non-polymers2,25611
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.743, 96.743, 238.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.691127, -0.675703, 0.256455), (-0.689934, 0.511146, -0.512562), (0.215254, -0.531183, -0.819458)51.2651, -0.75914, -68.0495
3given(0.551414, 0.798838, 0.240418), (0.803374, -0.586145, 0.104995), (0.224793, 0.13525, -0.964974)12.71897, -0.87589, -78.70512
4given(-0.879936, -0.120335, -0.4596), (-0.08996, -0.907689, 0.409889), (-0.466498, 0.402021, 0.787882)23.80202, 32.00024, -0.99308

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Components

#1: Protein
Tryptase alpha/beta-1 / Tryptase-1 / Tryptase I / Tryptase alpha-1


Mass: 27466.334 Da / Num. of mol.: 4 / Mutation: I118C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPSAB1, TPS1, TPS2, TPSB1 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q15661, tryptase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28ClN6O5 / References: GLU-GLY-ARG-CHLOROMETHYL KETONE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: ammonium sulfate, polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→37.57 Å / Num. obs: 35616 / Biso Wilson estimate: 79.2 Å2
Reflection shellResolution: 2.72→2.729 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3836 / CC1/2: 0.793 / Rpim(I) all: 0.545 / Rsym value: 1.246 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a0l

1a0l


Resolution: 2.72→37.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.705 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.685 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1034 2.9 %RANDOM
Rwork0.193 ---
obs0.194 35616 100 %-
Displacement parametersBiso mean: 59.82 Å2
Baniso -1Baniso -2Baniso -3
1--6.0504 Å20 Å20 Å2
2---6.0504 Å20 Å2
3---12.1009 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.72→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 135 25 7828
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0911066HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2568SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1172HARMONIC5
X-RAY DIFFRACTIONt_it8078HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion16.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion980SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8515SEMIHARMONIC4
LS refinement shellResolution: 2.72→2.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.25 -3.32 %
Rwork0.223 2794 -
all0.224 2890 -
obs--99.97 %

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