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- PDB-6h9i: Csf5, CRISPR-Cas type IV Cas6 crRNA endonuclease -

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Basic information

Entry
Database: PDB / ID: 6h9i
TitleCsf5, CRISPR-Cas type IV Cas6 crRNA endonuclease
Components
  • Csf5
  • crRNA
KeywordsRNA BINDING PROTEIN / type IV CRISPR-Cas / crRNA biogenesis / endonuclease
Function / homologymetal ion binding / : / L(+)-TARTARIC ACID / RNA / RNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesAromatoleum aromaticum (bacteria)
Aromatoleum aromaticum EbN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsPausch, P. / Bange, G.
CitationJournal: Nat Microbiol / Year: 2019
Title: Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum.
Authors: Ozcan, A. / Pausch, P. / Linden, A. / Wulf, A. / Schuhle, K. / Heider, J. / Urlaub, H. / Heimerl, T. / Bange, G. / Randau, L.
History
DepositionAug 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csf5
B: Csf5
C: crRNA
E: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,32311
Polymers75,5424
Non-polymers7817
Water1,982110
1
A: Csf5
C: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1635
Polymers37,7712
Non-polymers3923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-35 kcal/mol
Surface area14360 Å2
MethodPISA
2
B: Csf5
E: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1606
Polymers37,7712
Non-polymers3894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-31 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.850, 84.237, 71.472
Angle α, β, γ (deg.)90.00, 100.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCE

#1: Protein Csf5


Mass: 29695.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / Gene: p1B372 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5NWP0
#2: RNA chain crRNA


Mass: 8075.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aromatoleum aromaticum EbN1 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 117 molecules

#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-sodium tartrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.288→43.762 Å / Num. obs: 32620 / % possible obs: 98.29 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Net I/σ(I): 10.83
Reflection shellResolution: 2.29→2.37 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H9H

6h9h


Resolution: 2.29→43.762 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 3095 5.03 %
Rwork0.2232 --
obs0.2247 32603 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→43.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 1070 49 110 5145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045238
X-RAY DIFFRACTIONf_angle_d0.7927345
X-RAY DIFFRACTIONf_dihedral_angle_d13.2323014
X-RAY DIFFRACTIONf_chiral_restr0.044862
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2878-2.32360.38861280.40541972X-RAY DIFFRACTION71
2.3236-2.36170.36021270.36982702X-RAY DIFFRACTION96
2.3617-2.40240.3871540.3732749X-RAY DIFFRACTION97
2.4024-2.44610.38031420.36412688X-RAY DIFFRACTION97
2.4461-2.49310.37551730.33822722X-RAY DIFFRACTION98
2.4931-2.5440.38131420.33592768X-RAY DIFFRACTION98
2.544-2.59930.3151360.32772727X-RAY DIFFRACTION97
2.5993-2.65980.36381450.3022729X-RAY DIFFRACTION97
2.6598-2.72630.34181760.29492709X-RAY DIFFRACTION97
2.7263-2.80.31121240.28632707X-RAY DIFFRACTION96
2.8-2.88230.30541390.26532668X-RAY DIFFRACTION95
2.8823-2.97540.29881260.2492703X-RAY DIFFRACTION95
2.9754-3.08170.25741450.23742612X-RAY DIFFRACTION94
3.0817-3.2050.30321310.22992618X-RAY DIFFRACTION92
3.205-3.35080.24641380.22292544X-RAY DIFFRACTION91
3.3508-3.52740.2351150.21062750X-RAY DIFFRACTION96
3.5274-3.74830.2291760.19012677X-RAY DIFFRACTION97
3.7483-4.03750.20621620.18712717X-RAY DIFFRACTION97
4.0375-4.44350.22511250.1742730X-RAY DIFFRACTION97
4.4435-5.08570.16481280.1622667X-RAY DIFFRACTION95
5.0857-6.40420.2211380.18672557X-RAY DIFFRACTION91
6.4042-43.76960.18731250.1792760X-RAY DIFFRACTION97

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