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- PDB-5wtj: Crystal structure of an endonuclease -

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Basic information

Entry
Database: PDB / ID: 5wtj
TitleCrystal structure of an endonuclease
ComponentsCRISPR-associated endoribonuclease C2c2
KeywordsHYDROLASE
Function / homology: / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesLeptotrichia shahii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.503 Å
AuthorsLiu, L. / Wang, Y.
CitationJournal: Cell / Year: 2017
Title: Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities
Authors: Liu, L. / Li, X. / Wang, J. / Wang, M. / Chen, P. / Yin, M. / Li, J. / Sheng, G. / Wang, Y.
History
DepositionDec 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease C2c2
B: CRISPR-associated endoribonuclease C2c2


Theoretical massNumber of molelcules
Total (without water)336,7502
Polymers336,7502
Non-polymers00
Water181
1
A: CRISPR-associated endoribonuclease C2c2


Theoretical massNumber of molelcules
Total (without water)168,3751
Polymers168,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR-associated endoribonuclease C2c2


Theoretical massNumber of molelcules
Total (without water)168,3751
Polymers168,3751
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.658, 94.231, 338.218
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 C2c2 / EndoRNase / LshC2c2


Mass: 168374.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia shahii (strain DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37) (bacteria)
Strain: DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37
Gene: c2c2 / Production host: Escherichia coli (E. coli)
References: UniProt: P0DOC6, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.4M L-Proline, 0.1M HEPES pH 7.5, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 30634 / % possible obs: 97.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellRmerge(I) obs: 0.601

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHENIX1.8.2_1309phasing
HKL-3000data scaling
HKL-3000data processing
RefinementMethod to determine structure: SAD / Resolution: 3.503→48.375 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 1546 5.05 %
Rwork0.2626 --
obs0.264 30634 81.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→48.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15951 0 0 1 15952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916176
X-RAY DIFFRACTIONf_angle_d1.42121812
X-RAY DIFFRACTIONf_dihedral_angle_d23.1565989
X-RAY DIFFRACTIONf_chiral_restr0.0932488
X-RAY DIFFRACTIONf_plane_restr0.0062815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5034-3.61650.3842100.2578243X-RAY DIFFRACTION8
3.6165-3.74570.3014440.2546900X-RAY DIFFRACTION28
3.7457-3.89560.29831050.25792245X-RAY DIFFRACTION69
3.8956-4.07280.31381390.26172935X-RAY DIFFRACTION91
4.0728-4.28740.25761850.253126X-RAY DIFFRACTION97
4.2874-4.55580.30651760.24463158X-RAY DIFFRACTION98
4.5558-4.90730.25041800.24343186X-RAY DIFFRACTION99
4.9073-5.40050.28871650.27373250X-RAY DIFFRACTION99
5.4005-6.18060.35251940.30393248X-RAY DIFFRACTION100
6.1806-7.78170.32981830.31823321X-RAY DIFFRACTION100
7.7817-48.37940.25741650.24833476X-RAY DIFFRACTION99

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