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- PDB-7f84: Crystal structure of CRISPR-associated Cas2c of Leptospira interrogans -

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Basic information

Entry
Database: PDB / ID: 7f84
TitleCrystal structure of CRISPR-associated Cas2c of Leptospira interrogans
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsDNA BINDING PROTEIN / Leptospira / Cas2 / LinCas2C / CRISPR-Cas IC
Function / homologyCRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding / CRISPR-associated endoribonuclease Cas2
Function and homology information
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGogoi, P. / Anand, V. / Prabhakaran, H.S. / Kumar, M. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR25083/NER/95/1002/2017 India
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural and functional characterization of Cas2 of CRISPR-Cas subtype I-C lacking the CRISPR component.
Authors: Anand, V. / Prabhakaran, H.S. / Gogoi, P. / Kanaujia, S.P. / Kumar, M.
History
DepositionJul 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1803
Polymers21,0882
Non-polymers921
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-10 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.160, 103.160, 97.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: -1 - 87 / Label seq-ID: 1 - 89

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 10544.124 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Strain: Fiocruz L1-130 / Gene: cas2, LIC_12917 / Plasmid: pCDF1b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q72NB8, Hydrolases; Acting on ester bonds
#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.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.92 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.3 M sodium citrate tribasic dihydrate pH 5.6, 5% 2-propanol, 20% PEG 4000, 0.2% LMA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→72.94 Å / Num. obs: 8390 / % possible obs: 100 % / Redundancy: 16.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.04 / Rrim(I) all: 0.167 / Net I/σ(I): 12.3 / Num. measured all: 140737 / Scaling rejects: 333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.7216.90.5161710910110.9590.1290.5324.8100
9.01-72.9413.80.07633892460.9990.0220.0818.699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.83 Å72.94 Å
Translation3.83 Å72.94 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.4.1model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QR0

4qr0


Resolution: 2.6→72.94 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.875 / SU B: 21.105 / SU ML: 0.22 / SU R Cruickshank DPI: 0.4691 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 395 4.7 %RANDOM
Rwork0.2087 ---
obs0.2117 7993 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.68 Å2 / Biso mean: 39.872 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0 Å2
2---1.79 Å20 Å2
3---3.57 Å2
Refinement stepCycle: final / Resolution: 2.6→72.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 6 51 1479
Biso mean--63.98 33.52 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131452
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171442
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.6421949
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5893326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8665178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15922.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.95915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7481510
X-RAY DIFFRACTIONr_chiral_restr0.080.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02327
Refine LS restraints NCS

Ens-ID: 1 / Number: 2442 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 18 -
Rwork0.279 593 -
all-611 -
obs--100 %
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)
12.51990.51240.93512.04270.2043.2221-0.00280.0089-0.0986-0.1770.0769-0.1746-0.0080.0637-0.07410.02990.0070.03140.0221-0.00460.0919-11.394318.168-34.0842
21.6799-0.78440.19134.9746-0.62672.0560.0174-0.244-0.12480.6176-0.030.0575-0.1232-0.0680.01260.1-0.01950.02550.06010.00610.0756-17.858118.0871-18.8062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 87
2X-RAY DIFFRACTION2B-1 - 87

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