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- PDB-4dzd: Crystal structure of the CRISPR-associated protein Cas6e from Esc... -

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Basic information

Entry
Database: PDB / ID: 4dzd
TitleCrystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12
ComponentsUncharacterized protein ygcH
KeywordsHYDROLASE / ferredoxin-like domain / endoribonuclease / crRNA
Function / homology
Function and homology information


CRISPR-cas system / RNA processing / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / protein-containing complex / RNA binding
Similarity search - Function
Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR system Cascade subunit CasE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsWei, J. / Huang, G. / Wang, Y. / Gong, W.
CitationJournal: To be Published
Title: Crystal Structure of endoribonuclease Cas6e from Escherichia coli
Authors: Wei, J. / Huang, G. / Wang, Y. / Gong, W.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Uncharacterized protein ygcH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4492
Polymers24,3571
Non-polymers921
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 128.660
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 Uncharacterized protein ygcH / Cas6e


Mass: 24357.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygcH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q46897
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 16585 / Num. obs: 16585 / % possible obs: 99.9 % / Observed criterion σ(I): 21.5 / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.038.20.3717.2199.5
2.03-2.078.90.3386.61100
2.07-2.119.40.3066.31100
2.11-2.159.60.2786.11100
2.15-2.29.70.2565.91100
2.2-2.259.60.2115.81100
2.25-2.319.60.1915.61100
2.31-2.379.70.1735.31100
2.37-2.449.70.1535.11100
2.44-2.529.50.14251100
2.52-2.619.60.1294.91100
2.61-2.719.60.1184.81100
2.71-2.849.60.1034.91100
2.84-2.999.60.151100
2.99-3.179.50.0985.61100
3.17-3.429.50.1036.41100
3.42-3.769.40.10171100
3.76-4.319.30.0758.51100
4.31-5.439.10.0618.21100
5.43-508.30.0576.1198.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WJ9

1wj9


Resolution: 1.999→35.376 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8359 / SU ML: 0.43 / σ(F): 0 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 827 5 %
Rwork0.2019 15697 -
obs0.2042 16524 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.47 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 77.41 Å2 / Biso mean: 29.5102 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.7229 Å20 Å2-0 Å2
2--2.7229 Å2-0 Å2
3----5.4457 Å2
Refinement stepCycle: LAST / Resolution: 1.999→35.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 6 143 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061594
X-RAY DIFFRACTIONf_angle_d0.9862161
X-RAY DIFFRACTIONf_chiral_restr0.069243
X-RAY DIFFRACTIONf_plane_restr0.004279
X-RAY DIFFRACTIONf_dihedral_angle_d15.371610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9989-2.12410.26011520.20962501265399
2.1241-2.28810.21391190.197525782697100
2.2881-2.51830.25841260.195625912717100
2.5183-2.88250.23191280.204526042732100
2.8825-3.63110.26741320.199926492781100
3.6311-35.38180.2391700.203627742944100

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