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- PDB-4f3m: Crystal structure of CRISPR-associated protein -

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Basic information

Entry
Database: PDB / ID: 4f3m
TitleCrystal structure of CRISPR-associated protein
ComponentsBH0337 protein
KeywordsRNA BINDING PROTEIN / CRISPR / ferredoxin fold / endoribonuclease / RNA
Function / homology
Function and homology information


nuclease activity / maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Alpha-Beta Plaits - #2660 / CRISPR pre-crRNA endoribonuclease Cas5d / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
pre-crRNA processing endonuclease
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsKe, A. / Nam, K.H.
CitationJournal: Structure / Year: 2012
Title: Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System.
Authors: Nam, K.H. / Haitjema, C. / Liu, X. / Ding, F. / Wang, H. / Delisa, M.P. / Ke, A.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Data collection / Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: BH0337 protein
B: BH0337 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7129
Polymers54,2432
Non-polymers4687
Water7,837435
1
A: BH0337 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2803
Polymers27,1221
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BH0337 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4326
Polymers27,1221
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-35 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.509, 46.687, 129.030
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE OLIGOMERIC STATE HAS BEEN CHARACTERIZED AS MONOMER USING GEL-FILTRATION CHROMATOGRAPHY.

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Components

#1: Protein BH0337 protein


Mass: 27121.613 Da / Num. of mol.: 2
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: BH0337 / Plasmid: modified pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KFY3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 0.8 M Ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.977
SYNCHROTRONAPS 24-ID-C21
SYNCHROTRONAPS 24-ID-E30.98
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 29, 2010
ADSC QUANTUM 3152CCDJul 11, 2011
ADSC QUANTUM 3153CCDMar 24, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Cryo-Cooled double crystal. Si (111)SINGLE WAVELENGTHMx-ray2
3Cyrogenically-cooled single crystal Si(220) side bounce monochromamtorSINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
211
30.981
ReflectionResolution: 1.7→20 Å / Num. obs: 50063 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.73 Å / % possible all: 76.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.71→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.72 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 2553 5.1 %RANDOM
Rwork0.1525 ---
obs0.1565 50063 91.35 %-
all-50063 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.34 Å2 / Biso mean: 25.535 Å2 / Biso min: 8.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20.72 Å2
2---1.44 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 29 435 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023604
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9554850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07323.37184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89215595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3761524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212788
X-RAY DIFFRACTIONr_rigid_bond_restr7.433603
X-RAY DIFFRACTIONr_sphericity_free29.3515144
X-RAY DIFFRACTIONr_sphericity_bonded19.07753821
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 153 -
Rwork0.195 2771 -
all-2924 -
obs--74.01 %

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