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- PDB-6zq3: Crystal Structure of Silicatein Alpha from Marine Sponge Tethya a... -

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Basic information

Entry
Database: PDB / ID: 6zq3
TitleCrystal Structure of Silicatein Alpha from Marine Sponge Tethya aurantium
ComponentsSilicatein alpha
KeywordsHYDROLASE / Silica / Silicatein / Sponges / Demosponges / Spicules
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesTethya aurantium (orange puffball sponge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGoerlich, S. / Leonarski, R.J. / Tomizaki, T. / Zlotnikov, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z22EN11 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Natural hybrid silica/protein superstructure at atomic resolution.
Authors: Gorlich, S. / Samuel, A.J. / Best, R.J. / Seidel, R. / Vacelet, J. / Leonarski, F.K. / Tomizaki, T. / Rellinghaus, B. / Pohl, D. / Zlotnikov, I.
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Data collection / Database references / Category: citation / citation_author / diffrn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _diffrn.pdbx_serial_crystal_experiment
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Silicatein alpha


Theoretical massNumber of molelcules
Total (without water)23,2931
Polymers23,2931
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 59.600, 116.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Silicatein alpha


Mass: 23292.543 Da / Num. of mol.: 1 / Fragment: mature enzyme / Source method: isolated from a natural source / Details: tissue / Source: (natural) Tethya aurantium (orange puffball sponge) / References: UniProt: O76238
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 298 K / Method: in cell / Details: in vivo

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→51.5 Å / Num. obs: 9827 / % possible obs: 100 % / Redundancy: 159 % / CC1/2: 0.91 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 973 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
MOLREP6.4.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2VHS

2vhs


Resolution: 2.4→47.18 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.7 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.302 492 5 %RANDOM
Rwork0.2403 ---
obs0.2436 9337 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.98 Å2 / Biso mean: 49.104 Å2 / Biso min: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å2-0 Å2
2--1.46 Å20 Å2
3----4.74 Å2
Refinement stepCycle: final / Resolution: 2.4→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 24 1610
Biso mean---53.71 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191500
X-RAY DIFFRACTIONr_bond_other_d0.0010.021303
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9212040
X-RAY DIFFRACTIONr_angle_other_deg0.7932972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15224.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.532153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 36 -
Rwork0.372 673 -
all-709 -
obs--100 %

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