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- PDB-4qr1: Crystal structure of Streptococcus pyogenes Cas2 at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 4qr1
TitleCrystal structure of Streptococcus pyogenes Cas2 at pH 6.5
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsHYDROLASE / FERREDOXIN-LIKE FOLD / deoxyribonuclease
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 speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsBae, E. / Ka, D. / Kim, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions
Authors: Ka, D. / Kim, D. / Baek, G. / Bae, E.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2


Theoretical massNumber of molelcules
Total (without water)22,5242
Polymers22,5242
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-10 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.054, 55.054, 117.215
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: 11261.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas2, M5005_Spy1285, SPy_1561 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99YS8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 8000, 200mM Na acetate, 100mM Na cacodylate pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.193→50 Å / Num. obs: 9551 / % possible obs: 96.8 % / Redundancy: 12.8 % / Net I/σ(I): 15.55
Reflection shellResolution: 2.193→2.28 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 6.58 / Num. unique all: 951 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ES2

4es2


Resolution: 2.193→49.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.958 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26656 450 4.8 %RANDOM
Rwork0.20745 ---
obs0.21026 9459 96.34 %-
all-9818 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å20 Å2
2---0.8 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.193→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 49 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191376
X-RAY DIFFRACTIONr_bond_other_d0.0010.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9491857
X-RAY DIFFRACTIONr_angle_other_deg0.76233099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04522.64768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.151516
X-RAY DIFFRACTIONr_chiral_restr0.090.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
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_it2.7063.702658
X-RAY DIFFRACTIONr_mcbond_other2.7033.701657
X-RAY DIFFRACTIONr_mcangle_it3.7285.535819
X-RAY DIFFRACTIONr_mcangle_other3.7265.536820
X-RAY DIFFRACTIONr_scbond_it3.7944.219717
X-RAY DIFFRACTIONr_scbond_other3.7924.219718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7366.1321039
X-RAY DIFFRACTIONr_long_range_B_refined7.36530.2221564
X-RAY DIFFRACTIONr_long_range_B_other7.35730.0291547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 33 -
Rwork0.245 653 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.838-0.27740.60421.4329-0.21122.1059-0.07250.15950.0961-0.0615-0.0395-0.0192-0.24740.03710.11190.1135-0.0159-0.01260.04260.00810.0084-14.25416.3323-12.7882
22.2105-0.34371.12171.5714-0.80222.5808-0.2554-0.4037-0.02420.34680.2038-0.0545-0.1737-0.15560.05160.1440.0681-0.00120.1057-0.00410.0059-12.75461.94563.7483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 83
2X-RAY DIFFRACTION2B1 - 82

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