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- PDB-4es3: Double-stranded Endonuclease Activity in B. halodurans Clustered ... -

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Basic information

Entry
Database: PDB / ID: 4es3
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: 1.704 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: BH0342 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3702
Polymers11,3081
Non-polymers621
Water1,11762
1
A: BH0342 protein
hetero molecules

A: BH0342 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7404
Polymers22,6162
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3300 Å2
ΔGint-2 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.619, 37.904, 44.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 4% w/v PEG6000, 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: Nov 18, 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: 1.7→44.914 Å / Num. all: 10288 / Num. obs: 9508 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.73 Å / % possible all: 82.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.704→15.004 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8332 / SU ML: 0.17 / σ(F): 1.51 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 951 10 %RANDOM
Rwork0.2107 ---
obs0.2145 9507 92.61 %-
all-9515 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.584 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 127.85 Å2 / Biso mean: 30.2372 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.3695 Å2-0 Å20 Å2
2---6.6821 Å2-0 Å2
3---9.0516 Å2
Refinement stepCycle: LAST / Resolution: 1.704→15.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 4 62 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008678
X-RAY DIFFRACTIONf_angle_d1.027905
X-RAY DIFFRACTIONf_chiral_restr0.074108
X-RAY DIFFRACTIONf_plane_restr0.004111
X-RAY DIFFRACTIONf_dihedral_angle_d15.961261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.704-1.79390.28261200.25391084120484
1.7939-1.90610.26961240.21981113123786
1.9061-2.0530.24971340.22251205133993
2.053-2.25890.28721370.21881239137694
2.2589-2.58440.25081370.21541222135994
2.5844-3.25060.24111470.20551325147299
3.2506-15.00420.23551520.20211368152097
Refinement TLS params.Method: refined / Origin x: -8.6625 Å / Origin y: 0.7688 Å / Origin z: -14.4096 Å
111213212223313233
T0.1409 Å20.0037 Å20.0135 Å2-0.1435 Å20.0043 Å2--0.1283 Å2
L1.7614 °2-0.1237 °20.65 °2-1.4597 °2-0.2306 °2--0.6434 °2
S0.006 Å °-0.1623 Å °-0.0646 Å °0.1008 Å °0.0384 Å °0.1999 Å °0.0757 Å °-0.1025 Å °0.0008 Å °
Refinement TLS groupSelection details: all

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