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- PDB-4h7a: Crystal structure of CasB from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 4h7a
TitleCrystal structure of CasB from Thermus thermophilus
ComponentsCRISPR-associated protein Cse2
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 / defense response to virus / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein Cse2
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated protein Cse2
B: CRISPR-associated protein Cse2


Theoretical massNumber of molelcules
Total (without water)38,8462
Polymers38,8462
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.777, 100.777, 84.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 156 / Label seq-ID: 13 - 168

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsBiological Assembly has been characterized by electron microscopy

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Components

#1: Protein CRISPR-associated protein Cse2 / CRISPR type I-E/ECOLI-associated protein CasB/Cse2


Mass: 19423.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cse2, TTHB189 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q53VY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M MES, pH 5.7-5.9, 50 mM MgSO4, 5% (w/v) PEG 3350, 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: Oct 31, 2011
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: 2.6→30 Å / Num. obs: 12996 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.64 Å / % possible all: 86.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2zca


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.427 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 638 4.9 %RANDOM
Rwork0.1734 ---
obs0.176 12973 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.38 Å2 / Biso mean: 64.2504 Å2 / Biso min: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 0 10 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192608
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9413524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8095307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89921.223139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.19415424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9741538
X-RAY DIFFRACTIONr_chiral_restr0.110.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212058
X-RAY DIFFRACTIONr_rigid_bond_restr13.92432608
X-RAY DIFFRACTIONr_sphericity_free14.34654
X-RAY DIFFRACTIONr_sphericity_bonded43.10752547
Refine LS restraints NCS

Ens-ID: 1 / Number: 159 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.19 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 42 -
Rwork0.29 764 -
all-806 -
obs--86.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00460.01320.0040.03930.01190.00360.00050.0008-0.0019-0.0091-0.0014-0.0029-0.0024-0.00120.00090.07550.01420.00010.096-0.00180.0258-11.3467-39.8523-3.8323
20.3509-0.0503-0.30690.26640.2770.49670.03-0.1217-0.0245-0.0403-0.019-0.0161-0.03230.051-0.0110.0564-0.0318-0.01260.0780.02350.0385-35.6581-36.121923.7493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2B1 - 156

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