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- PDB-4es1: Double-stranded Endonuclease Activity in B. halodurans Clustered ... -

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Basic information

Entry
Database: PDB / ID: 4es1
TitleDouble-stranded Endonuclease Activity in B. halodurans Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas2 Protein
ComponentsBH0342 protein
KeywordsHYDROLASE / ferredoxin / nuclease
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / magnesium ion binding / protein homodimerization activity
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas2
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsKe, A. / Nam, K.H.
CitationJournal: J. Biol. Chem. / Year: 2012
Title: Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein.
Authors: Nam, K.H. / Ding, F. / Haitjema, C. / Huang, Q. / DeLisa, M.P. / Ke, A.
History
DepositionApr 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 28, 2018Group: Data collection / 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH0342 protein


Theoretical massNumber of molelcules
Total (without water)11,3081
Polymers11,3081
Non-polymers00
Water2,072115
1
A: BH0342 protein

A: BH0342 protein


Theoretical massNumber of molelcules
Total (without water)22,6162
Polymers22,6162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2760 Å2
ΔGint-9 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.887, 33.440, 39.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BH0342 protein


Mass: 11308.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH0342 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star
References: UniProt: Q9KFX8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 2% w/v PEG2000 MME, 10 mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.1→10 Å / Num. all: 35849 / Num. obs: 34580 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.1→1.12 Å / % possible all: 86.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.61 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16435 1723 5 %RANDOM
Rwork0.15774 ---
obs0.15807 32857 96.64 %-
all-34593 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 0 0 115 864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022771
X-RAY DIFFRACTIONr_bond_other_d0.0120.02533
X-RAY DIFFRACTIONr_angle_refined_deg2.2661.9781036
X-RAY DIFFRACTIONr_angle_other_deg1.31331308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.794595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.83424.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.548155
X-RAY DIFFRACTIONr_chiral_restr0.2380.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.31.5476
X-RAY DIFFRACTIONr_mcbond_other1.0931.5195
X-RAY DIFFRACTIONr_mcangle_it3.2982771
X-RAY DIFFRACTIONr_scbond_it4.6573295
X-RAY DIFFRACTIONr_scangle_it6.3814.5265
X-RAY DIFFRACTIONr_rigid_bond_restr2.18531304
X-RAY DIFFRACTIONr_sphericity_free13.2393115
X-RAY DIFFRACTIONr_sphericity_bonded5.76831294
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 117 -
Rwork0.168 2150 -
obs--88.21 %

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