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- PDB-4h79: Crystal structure of CasB from Thermobifida fusca -

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Basic information

Entry
Database: PDB / ID: 4h79
TitleCrystal structure of CasB from Thermobifida fusca
ComponentsCRISPR-associated protein, Cse2 family
KeywordsDNA BINDING PROTEIN / CRISPR / Cascade / CasB / CRISPR-assoicated protein / Nucleic acid binding protein
Function / homologyCRISPR-associated protein Cse2 / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein, Cse2 family
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKe, A. / Nam, K.H.
CitationJournal: Febs Lett. / Year: 2012
Title: Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures.
Authors: Nam, K.H. / Huang, Q. / Ke, A.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: CRISPR-associated protein, Cse2 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8073
Polymers24,6831
Non-polymers1242
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.749, 86.749, 70.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CRISPR-associated protein, Cse2 family


Mass: 24682.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1599 / Plasmid: modified pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q47PI5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, pH 8.0-8.5, 2% (v/v) ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

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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 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 22861 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 78.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZCA

2zca


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.507 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1171 5.1 %RANDOM
Rwork0.1476 ---
all0.15 ---
obs0.15 22848 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.48 Å2 / Biso mean: 37.0509 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.01 Å20 Å2
2--2.03 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 8 89 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191476
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9521988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08321.28278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9891524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211137
X-RAY DIFFRACTIONr_rigid_bond_restr10.77631476
X-RAY DIFFRACTIONr_sphericity_free28.111525
X-RAY DIFFRACTIONr_sphericity_bonded29.76551517
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 68 -
Rwork0.198 1331 -
all-1399 -
obs--80.26 %
Refinement TLS params.Method: refined / Origin x: -29.2936 Å / Origin y: 32.5466 Å / Origin z: 9.8554 Å
111213212223313233
T0.0189 Å2-0.0079 Å20.0011 Å2-0.0194 Å2-0.0031 Å2--0.0074 Å2
L0.209 °20.0195 °20.2033 °2-0.032 °2-0.1884 °2--1.6712 °2
S0.0174 Å °-0.0221 Å °0.0173 Å °0.0072 Å °-0.0245 Å °0.003 Å °-0.0503 Å °0.1364 Å °0.007 Å °

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