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- PDB-3qhq: Structure of CRISPR-associated protein Csn2 -

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Basic information

Entry
Database: PDB / ID: 3qhq
TitleStructure of CRISPR-associated protein Csn2
ComponentsSag0897 family CRISPR-associated protein
KeywordsTRANSFERASE / Helicase
Function / homology
Function and homology information


defense response to virus / DNA binding / metal ion binding
Similarity search - Function
Rossmann fold - #11940 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2340 / CRISPR-associated protein, Csn2-type / CRISPR-associated protein Csn2 superfamily / CRISPR-associated protein (Cas_Csn2) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated protein Csn2
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsEllinger, P. / Arslan, Z. / Wurm, R. / Tschapek, B. / Pfeffer, K. / Wagner, R. / Schmitt, L. / Pul, U. / Smits, S.H.
CitationJournal: To be Published
Title: Structure of CRISPR-associated protein Csn2
Authors: Ellinger, P. / Arslan, Z. / Wurm, R. / Tschapek, B. / Pfeffer, K. / Wagner, R. / Schmitt, L. / Pul, U. / Smits, S.H.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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.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_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: Sag0897 family CRISPR-associated protein
B: Sag0897 family CRISPR-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,84010
Polymers53,4542
Non-polymers3878
Water5,332296
1
A: Sag0897 family CRISPR-associated protein
B: Sag0897 family CRISPR-associated protein
hetero molecules

A: Sag0897 family CRISPR-associated protein
B: Sag0897 family CRISPR-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,68120
Polymers106,9084
Non-polymers77316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12390 Å2
ΔGint-85 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 83.300, 110.400
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sag0897 family CRISPR-associated protein / Csn2


Mass: 26726.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: ATCC 13813 / Gene: HMPREF9171_1216 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7S4M0, DNA-directed RNA polymerase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONFLICTS I2V, V133A AND N157H WERE CONSIDERED TO BE NATURALLY OCCURRING POLYMORPHISM.

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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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Hepes, 12% PEG 6000, 0.05M Phenole, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979981 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979981 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43206 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.53 % / Biso Wilson estimate: 33.334 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 36.51
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.39 / Num. unique all: 3103 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BESTdata collection
Auto-Rickshawphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.663 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 2174 5 %RANDOM
Rwork0.2036 ---
obs0.2048 41031 99.42 %-
all-43206 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.4208 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20.64 Å2
2--1.12 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 17 296 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223655
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9954970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8575454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10126.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87615686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.786154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212672
X-RAY DIFFRACTIONr_mcbond_it0.3611.52237
X-RAY DIFFRACTIONr_mcangle_it0.67123665
X-RAY DIFFRACTIONr_scbond_it0.99431418
X-RAY DIFFRACTIONr_scangle_it1.6764.51305
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 141 -
Rwork0.224 2940 -
obs--97.32 %
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)
12.5890.5011-0.36082.1844-0.76633.38790.0649-0.06560.0272-0.03610.10560.17330.03860.0451-0.17040.1223-0.088-0.0230.1364-0.02070.116224.58743.21933.511
22.15110.3151-1.64660.9677-0.53663.79370.23020.2905-0.0207-0.0385-0.1315-0.0650.0769-0.3097-0.09870.11180.1075-0.03140.30870.02710.100213.92344.434-6.636
33.5880.512-1.15672.607-0.31222.5810.4486-0.24080.9480.1149-0.05490.2372-0.83560.3774-0.39370.4451-0.25060.13810.2243-0.13510.377236.29364.62931.775
42.3527-0.2004-1.36281.05480.54453.13590.4821-0.28710.32420.077-0.1682-0.0245-0.42520.3706-0.3140.1922-0.1420.04780.2965-0.05930.132163.64953.4156.02
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 72
2X-RAY DIFFRACTION1A138 - 221
3X-RAY DIFFRACTION2A73 - 137
4X-RAY DIFFRACTION3B1 - 72
5X-RAY DIFFRACTION3B138 - 215
6X-RAY DIFFRACTION4B73 - 137

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