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- PDB-4z7k: Crystal structure of CRISPR RNA processing endoribonuclease Cas6b -

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Basic information

Entry
Database: PDB / ID: 4z7k
TitleCrystal structure of CRISPR RNA processing endoribonuclease Cas6b
Components
  • Cas6b
  • RNA/DNA Hybrid (31-MER)
KeywordsHydrolase/RNA/DNA / Cas6 / endoribonuclease / CRISPR RNA / Hydrolase-RNA-DNA complex
Function / homologyCas6b, C-terminal domain / Cas6b N-terminal / Cas6b C-terminal domain / Cas6b N-terminal domain / identical protein binding / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA repair protein
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM099604 United States
CitationJournal: Structure / Year: 2016
Title: A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6.
Authors: Shao, Y. / Richter, H. / Sun, S. / Sharma, K. / Urlaub, H. / Randau, L. / Li, H.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 29, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _entity.src_method
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Cas6b
A: Cas6b
C: RNA/DNA Hybrid (31-MER)


Theoretical massNumber of molelcules
Total (without water)61,0613
Polymers61,0613
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-19 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.122, 92.122, 96.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Cas6b


Mass: 25555.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (strain C5 / ATCC BAA-1333) (archaea)
Strain: C5 / ATCC BAA-1333 / Gene: MmarC5_0767 / Production host: Escherichia coli (E. coli) / References: UniProt: A4FXZ3
#2: DNA/RNA hybrid RNA/DNA Hybrid (31-MER)


Mass: 9950.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Methanococcus maripaludis (archaea)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop
Details: 100 mM KCl, 10mM MgCl2, 50mM sodium cacodylate pH 6.5, 12% PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16169 / % possible obs: 83.6 % / Redundancy: 4.8 % / Net I/σ(I): 36.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.592 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 3320 10.11 %
Rwork0.2239 --
obs0.2294 32843 89.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 531 0 0 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014055
X-RAY DIFFRACTIONf_angle_d1.7175563
X-RAY DIFFRACTIONf_dihedral_angle_d20.1851620
X-RAY DIFFRACTIONf_chiral_restr0.077623
X-RAY DIFFRACTIONf_plane_restr0.007612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04280.4129570.3535501X-RAY DIFFRACTION36
3.0428-3.08820.3518870.3405718X-RAY DIFFRACTION52
3.0882-3.13650.5011770.3437768X-RAY DIFFRACTION56
3.1365-3.18790.5047970.3427953X-RAY DIFFRACTION67
3.1879-3.24280.31661250.341011X-RAY DIFFRACTION73
3.2428-3.30180.37621190.31981120X-RAY DIFFRACTION82
3.3018-3.36530.34211180.33691215X-RAY DIFFRACTION88
3.3653-3.43390.3961520.31131321X-RAY DIFFRACTION95
3.4339-3.50860.35941470.2791307X-RAY DIFFRACTION96
3.5086-3.59010.35571370.26721399X-RAY DIFFRACTION98
3.5901-3.67990.31491600.29961352X-RAY DIFFRACTION100
3.6799-3.77930.29691560.2731345X-RAY DIFFRACTION100
3.7793-3.89040.39421600.27121376X-RAY DIFFRACTION100
3.8904-4.01590.35571720.26291382X-RAY DIFFRACTION100
4.0159-4.15930.29111520.23811390X-RAY DIFFRACTION100
4.1593-4.32570.26771680.2071376X-RAY DIFFRACTION100
4.3257-4.52230.30281600.19551318X-RAY DIFFRACTION100
4.5223-4.76040.23291680.18831386X-RAY DIFFRACTION100
4.7604-5.05820.22221520.17931386X-RAY DIFFRACTION100
5.0582-5.44790.24751560.19791390X-RAY DIFFRACTION100
5.4479-5.99470.25631340.21811374X-RAY DIFFRACTION100
5.9947-6.85880.30111640.22641359X-RAY DIFFRACTION100
6.8588-8.62870.20791440.20551395X-RAY DIFFRACTION100
8.6287-41.59560.23781580.18221381X-RAY DIFFRACTION99

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