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- PDB-4wj0: Structure of PH1245, a cas1 from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 4wj0
TitleStructure of PH1245, a cas1 from Pyrococcus horikoshii
ComponentsCRISPR-associated endonuclease Cas1
KeywordsIMMUNE SYSTEM / CRISPR-ASSOCIATED CAS1 / METALLONUCLEASE / DNASE / PROK IMMUNE SYSTEM / NUCLEASE
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, HMARI/TNEAP subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...CRISPR-associated protein Cas1, HMARI/TNEAP subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPetit, P. / Brown, G. / Savchenko, A. / Yakunin, A.F.
CitationJournal: To Be Published
Title: Structure of PH1245, a cas1 from Pyrococcus horikoshii
Authors: Petit, P. / Brown, G. / Savchenko, A. / Yakunin, A.F.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionOct 15, 2014ID: 3PV9
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7044
Polymers75,6332
Non-polymers712
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-39 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.890, 58.672, 90.147
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 endonuclease Cas1


Mass: 37816.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: cas1, PH1245 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O58938, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 19% PEG 3350, 0.1M CITRIC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→29.34 Å / Num. obs: 15944 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.13 / Rsym value: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LFX

3lfx
PDB Unreleased entry


Resolution: 2.85→29.336 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 796 5 %Random
Rwork0.2266 ---
obs0.2294 15923 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 2 21 5165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075248
X-RAY DIFFRACTIONf_angle_d1.1217075
X-RAY DIFFRACTIONf_dihedral_angle_d15.0112000
X-RAY DIFFRACTIONf_chiral_restr0.044781
X-RAY DIFFRACTIONf_plane_restr0.007892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-3.02850.35111500.29742492X-RAY DIFFRACTION100
3.0285-3.2620.33621240.28042523X-RAY DIFFRACTION100
3.262-3.58980.32091310.2562506X-RAY DIFFRACTION99
3.5898-4.1080.30031430.21332487X-RAY DIFFRACTION98
4.108-5.1710.25131240.18622511X-RAY DIFFRACTION97
5.171-29.33750.23111240.21912608X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 16.2722 Å / Origin y: -39.2619 Å / Origin z: 6.3532 Å
111213212223313233
T0.2713 Å2-0.07 Å20.039 Å2-0.2948 Å2-0.0883 Å2--0.2956 Å2
L1.2517 °2-0.6309 °2-0.0807 °2-1.263 °2-0.5682 °2--1.336 °2
S-0.0306 Å °0.2465 Å °-0.1008 Å °0.0694 Å °0.0486 Å °0.1408 Å °0.025 Å °-0.1563 Å °-0.0114 Å °
Refinement TLS groupSelection details: all

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