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- PDB-4tno: Hypothetical protein PF1117 from Pyrococcus Furiosus: Structure s... -

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Basic information

Entry
Database: PDB / ID: 4tno
TitleHypothetical protein PF1117 from Pyrococcus Furiosus: Structure solved by sulfur-SAD using Swiss Light Source Data
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsHYDROLASE / SULFUR SAD
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsWeinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0643
Polymers9,9931
Non-polymers712
Water1629
1
A: CRISPR-associated endoribonuclease Cas2
hetero molecules

A: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1276
Polymers19,9852
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3510 Å2
ΔGint-50 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.210, 47.210, 82.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 9992.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cas2, PF1117 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8U1T8, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M SODIUM CITRATE BUFFER CONTAINING 0.1 M CHES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 10426 / % possible obs: 97.1 % / Redundancy: 76.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 71.7
Reflection shellRedundancy: 3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.2 / % possible all: 65.2

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDEphasing
CootFOLLOWED BY PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
SHELXCDphasing
SHELXDphasing
SHELXEFOLLOWED BY PHENIXmodel building
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.14→40.948 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 0.3861 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3053 943 9.83 %
Rwork0.2525 --
obs0.2577 9591 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→40.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 2 9 704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01704
X-RAY DIFFRACTIONf_angle_d1.338947
X-RAY DIFFRACTIONf_dihedral_angle_d19.321276
X-RAY DIFFRACTIONf_chiral_restr0.05108
X-RAY DIFFRACTIONf_plane_restr0.009119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.24680.39561060.33011030X-RAY DIFFRACTION80
2.2468-2.38760.42081270.30331272X-RAY DIFFRACTION100
2.3876-2.57190.36761460.32651271X-RAY DIFFRACTION100
2.5719-2.83070.51241440.34051246X-RAY DIFFRACTION100
2.8307-3.24010.3241500.2971267X-RAY DIFFRACTION100
3.2401-4.08160.29431400.24861275X-RAY DIFFRACTION100
4.0816-40.95590.24261300.20781287X-RAY DIFFRACTION100

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