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- PDB-3s4l: The CRISPR-associated Cas3 HD domain protein MJ0384 from Methanoc... -

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Basic information

Entry
Database: PDB / ID: 3s4l
TitleThe CRISPR-associated Cas3 HD domain protein MJ0384 from Methanocaldococcus jannaschii
ComponentsCAS3 Metal dependent phosphohydrolase
KeywordsHYDROLASE / IMMUNE SYSTEM / HD-MOTIF / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Nuclease
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
Hypothetical protein af1432 - #30 / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / Cas3, HD domain / HD Cas3-type domain profile. / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas3-HD
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPetit, P. / Brown, G. / Yakunin, A. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Embo J. / Year: 2011
Title: Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference.
Authors: Beloglazova, N. / Petit, P. / Flick, R. / Brown, G. / Savchenko, A. / Yakunin, A.F.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJun 22, 2011ID: 3M5F
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Structure summary
Revision 1.3Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAS3 Metal dependent phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5333
Polymers28,4531
Non-polymers802
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.073, 59.073, 162.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CAS3 Metal dependent phosphohydrolase / Uncharacterized protein MJ0384


Mass: 28452.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0384, Y384_METJA / Plasmid: p15-TVL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57829
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / pH: 6
Details: PEG 5000 MME 25%, (NH4)2 SO4 0.2M, SPG 0.1M, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97941
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.3→29.54 Å / Num. obs: 13603 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 38.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.537 Å / SU ML: 0.64 / σ(F): 1.35 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 671 4.96 %
Rwork0.2336 --
obs0.2355 13536 99.87 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.389 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.9399 Å20 Å2-0 Å2
2--3.9399 Å20 Å2
3----7.8798 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 2 30 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081609
X-RAY DIFFRACTIONf_angle_d1.1222162
X-RAY DIFFRACTIONf_dihedral_angle_d18.409601
X-RAY DIFFRACTIONf_chiral_restr0.084255
X-RAY DIFFRACTIONf_plane_restr0.003262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47750.39371430.29172499X-RAY DIFFRACTION100
2.4775-2.72670.27041360.2592498X-RAY DIFFRACTION100
2.7267-3.12090.32471270.24722560X-RAY DIFFRACTION100
3.1209-3.93050.28641420.23432569X-RAY DIFFRACTION100
3.9305-29.53890.22421230.21382739X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 48.8527 Å / Origin y: 24.4472 Å / Origin z: 80.1563 Å
111213212223313233
T0.0449 Å2-0.0542 Å2-0.033 Å2-0.0903 Å20.0525 Å2--0.0968 Å2
L2.3864 °20.8711 °2-1.2064 °2-2.7604 °2-1.997 °2--3.837 °2
S-0.0923 Å °0.2082 Å °-0.0155 Å °-0.0228 Å °0.2092 Å °0.0509 Å °0.1053 Å °-0.1806 Å °-0.0472 Å °
Refinement TLS groupSelection details: all

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