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- PDB-3oq2: Structure of a CRISPR associated protein Cas2 from Desulfovibrio ... -

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Basic information

Entry
Database: PDB / ID: 3oq2
TitleStructure of a CRISPR associated protein Cas2 from Desulfovibrio vulgaris
ComponentsCRISPR-associated protein Cas2
KeywordsIMMUNE SYSTEM / Ferredoxin fold / CRISPR
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
CITRIC ACID / CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsSamai, P. / Smith, P. / Shuman, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris.
Authors: Samai, P. / Smith, P. / Shuman, S.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2017Group: Refinement description / Category: refine
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein Cas2
B: CRISPR-associated protein Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,13113
Polymers23,8932
Non-polymers1,23711
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CRISPR-associated protein Cas2
B: CRISPR-associated protein Cas2
hetero molecules

A: CRISPR-associated protein Cas2
B: CRISPR-associated protein Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26126
Polymers47,7874
Non-polymers2,47522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11780 Å2
ΔGint-172 kcal/mol
Surface area18120 Å2
MethodPISA
3
A: CRISPR-associated protein Cas2
hetero molecules

A: CRISPR-associated protein Cas2
hetero molecules

B: CRISPR-associated protein Cas2
hetero molecules

B: CRISPR-associated protein Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26126
Polymers47,7874
Non-polymers2,47522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8250 Å2
ΔGint-182 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.874, 48.810, 41.320
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-105-

CL

21A-112-

SO4

31A-246-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CRISPR-associated protein Cas2


Mass: 11946.675 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: cas2, DVUA0135 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72WF4

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Non-polymers , 6 types, 329 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein solution 0.85 mM DvuCas2, reservoir solution 1 M lithium sulfate, 0.5 M ammonium sulfate and 0.1 M trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 46959 / Num. obs: 45550 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.049 / Net I/σ(I): 29.1
Reflection shellResolution: 1.35→50 Å / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.35→29.079 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 15.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 2146 4.97 %
Rwork0.1277 --
obs0.1302 43191 92.58 %
all-46653 -
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.873 Å2 / ksol: 0.446 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7097 Å2-0 Å20.325 Å2
2---0.6712 Å2-0 Å2
3---1.418 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 74 318 1997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061827
X-RAY DIFFRACTIONf_angle_d1.1192499
X-RAY DIFFRACTIONf_dihedral_angle_d14.386711
X-RAY DIFFRACTIONf_chiral_restr0.066252
X-RAY DIFFRACTIONf_plane_restr0.005321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.24851800.17363313X-RAY DIFFRACTION75
1.3983-1.45420.19141860.13713795X-RAY DIFFRACTION86
1.4542-1.52040.17992040.12123965X-RAY DIFFRACTION89
1.5204-1.60060.15792240.10674113X-RAY DIFFRACTION93
1.6006-1.70080.17121920.10644189X-RAY DIFFRACTION96
1.7008-1.83210.16092100.11374306X-RAY DIFFRACTION97
1.8321-2.01650.17542360.11234305X-RAY DIFFRACTION97
2.0165-2.30820.17132510.11144346X-RAY DIFFRACTION98
2.3082-2.90760.16852360.12974364X-RAY DIFFRACTION98
2.9076-29.08540.18522270.14544349X-RAY DIFFRACTION96

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