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- PDB-5an6: Crystal structure of Thermotoga maritima Csm2 -

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Basic information

Entry
Database: PDB / ID: 5an6
TitleCrystal structure of Thermotoga maritima Csm2
ComponentsCRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY
KeywordsDNA BINDING PROTEIN / CRISPR-CAS / CD-SAD
Function / homologyCRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / defense response to virus / RNA binding / : / CRISPR system Cms protein Csm2
Function and homology information
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.403 Å
AuthorsGallo, G. / Augusto, G. / Rangel, G. / Zelanis, A. / Mori, M.A. / Campos, C.B. / Wurtele, M.
CitationJournal: FEBS J. / Year: 2016
Title: Structural Basis for Dimer Formation of the Crispr-Associated Protein Csm2 of Thermotoga Maritima.
Authors: Gallo, G. / Augusto, G. / Rangel, G. / Zelanis, A. / Mori, M.A. / Campos, C.B. / Wurtele, M.
History
DepositionSep 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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, CSM2 FAMILY
B: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY
C: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,07010
Polymers44,2833
Non-polymers7877
Water2,000111
1
B: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY
C: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3099
Polymers29,5222
Non-polymers7877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-94.5 kcal/mol
Surface area13070 Å2
MethodPISA
2
A: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY

A: CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY


Theoretical massNumber of molelcules
Total (without water)29,5222
Polymers29,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8660 Å2
ΔGint-71.1 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.000, 77.000, 160.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CRISPR-ASSOCIATED PROTEIN, CSM2 FAMILY / CSM2


Mass: 14760.979 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 6-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X2D0
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 100MM SODIUM ACETATE PH 4.6 100MM CADMIUM CHLORIDE 21% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21688 / % possible obs: 98.3 % / Observed criterion σ(I): 12.63 / Redundancy: 6.24 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.63
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.03 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.64 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.403→41.651 Å / SU ML: 0.26 / σ(F): 1.38 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1119 5.2 %
Rwork0.2098 --
obs0.2119 21679 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→41.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 7 111 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093198
X-RAY DIFFRACTIONf_angle_d1.1114275
X-RAY DIFFRACTIONf_dihedral_angle_d16.691245
X-RAY DIFFRACTIONf_chiral_restr0.042444
X-RAY DIFFRACTIONf_plane_restr0.005540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4033-2.51270.28821260.23522384X-RAY DIFFRACTION93
2.5127-2.64510.29461360.22212529X-RAY DIFFRACTION98
2.6451-2.81080.31211190.22532543X-RAY DIFFRACTION98
2.8108-3.02780.27641310.23482553X-RAY DIFFRACTION99
3.0278-3.33240.25891310.2352598X-RAY DIFFRACTION99
3.3324-3.81430.26121370.19882603X-RAY DIFFRACTION99
3.8143-4.80440.21241740.18082616X-RAY DIFFRACTION100
4.8044-41.65680.23921650.2122734X-RAY DIFFRACTION99

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