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- PDB-4q2c: Crystal structure of CRISPR-associated protein -

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Basic information

Entry
Database: PDB / ID: 4q2c
TitleCrystal structure of CRISPR-associated protein
ComponentsCRISPR-associated helicase Cas3
KeywordsHYDROLASE / RecA / HD nuclease
Function / homology
Function and homology information


defense response to virus / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Cas3, C-terminal / Hypothetical protein af1432 - #30 / Cas3 C-terminal domain / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : ...Cas3, C-terminal / Hypothetical protein af1432 - #30 / Cas3 C-terminal domain / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : / Hypothetical protein af1432 / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / CRISPR-associated helicase Cas3
Similarity search - Component
Biological speciesThermobaculum terrenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsGong, B. / Shin, M. / Sun, J. / van der Oost, J. / Kim, J.-S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3.
Authors: Gong, B. / Shin, M. / Sun, J. / Jung, C.H. / Bolt, E.L. / van der Oost, J. / Kim, J.S.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated helicase Cas3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3274
Polymers105,1511
Non-polymers1763
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.268, 214.558, 102.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1168-

HOH

21A-1205-

HOH

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Components

#1: Protein CRISPR-associated helicase Cas3 / nuclease


Mass: 105150.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (bacteria) / Strain: ATCC BAA-798 / Gene: Tter_1895 / Production host: Escherichia coli (E. coli) / References: UniProt: D1CGD0
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2M Sodium Chloride, 0.1M Sodium phosphate monobasic monohydrate, 0.1M Potassium phosphate monobasic, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 37133 / % possible obs: 93.3 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 41.55 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→93.781 Å / FOM work R set: 0.8315 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1871 5 %RANDOM
Rwork0.191 ---
obs0.193 34571 93.43 %-
all-37404 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.86 Å2 / Biso mean: 51.87 Å2 / Biso min: 21.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→93.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 3 282 7487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047380
X-RAY DIFFRACTIONf_angle_d0.94810057
X-RAY DIFFRACTIONf_chiral_restr0.0721109
X-RAY DIFFRACTIONf_plane_restr0.0041318
X-RAY DIFFRACTIONf_dihedral_angle_d15.3092706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.56770.27871460.25622769291596
2.5677-2.64320.30281450.25132752289796
2.6432-2.72860.31651450.24412772291796
2.7286-2.82610.30671460.23332758290495
2.8261-2.93920.27081440.22392740288495
2.9392-3.0730.26931450.20862747289295
3.073-3.23510.22251430.20362728287194
3.2351-3.43770.24281440.19062722286693
3.4377-3.70320.21291430.17662732287593
3.7032-4.07590.21491430.16612706284993
4.0759-4.66560.1741420.15372700284292
4.6656-5.87810.20721430.17992717286091
5.8781-93.84660.21981420.18892690283287
Refinement TLS params.Method: refined / Origin x: -28.1386 Å / Origin y: 29.1536 Å / Origin z: -3.4831 Å
111213212223313233
T0.2908 Å2-0.0225 Å2-0.0033 Å2-0.289 Å20.0335 Å2--0.2566 Å2
L0.3909 °20.3067 °20.1532 °2-1.3405 °20.6946 °2--0.9671 °2
S-0.0228 Å °-0.0344 Å °0.0137 Å °0.0125 Å °0.0488 Å °-0.0583 Å °0.0269 Å °0.1666 Å °-0.026 Å °
Refinement TLS groupSelection details: ALL

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