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- PDB-4mak: Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR a... -

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Basic information

Entry
Database: PDB / ID: 4mak
TitleCrystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsHYDROLASE / CAS2 / CRISPR / MCSG / PSI-BIOLOGY / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


CRISPR-cas system / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
CRISPR-associated protein Cas2 subtype / CRISPR-associated protein (Cas_Cas2CT1978) / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsNocek, B. / Skarina, T. / Brown, G. / Yakunin, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative ssRNA endonuclease Cas2, CRISPR adaptation protein from E.coli
Authors: Nocek, B. / Skarina, T. / Brown, G. / Yakunin, A. / Joachimiak, A.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1613
Polymers21,0542
Non-polymers1061
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-19 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.048, 66.009, 69.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 10527.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 substr. MG1655 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45956, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.65 Å3/Da / Density % sol: 25.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG3350, 0.1M KCl, 10mM MgCl2, Na Citr 0.1M ph 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.1→33.03 Å / Num. all: 57350 / Num. obs: 53336 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 28
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.43 / % possible all: 52

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
CCP4model building
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→33.03 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.863 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.034 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17333 2427 5.1 %RANDOM
Rwork0.1324 ---
all0.136 47580 --
obs0.13629 45153 83.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.1→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 7 231 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021210
X-RAY DIFFRACTIONr_bond_other_d0.0010.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9411648
X-RAY DIFFRACTIONr_angle_other_deg0.84632703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.685153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24823.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70815201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5581511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.26332396
X-RAY DIFFRACTIONr_sphericity_free37.657518
X-RAY DIFFRACTIONr_sphericity_bonded12.0152591
LS refinement shellResolution: 1.101→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 49 -
Rwork0.245 812 -
obs--20.68 %

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