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- PDB-2xvo: SSO1725, a protein involved in the CRISPR/Cas pathway -

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Basic information

Entry
Database: PDB / ID: 2xvo
TitleSSO1725, a protein involved in the CRISPR/Cas pathway
ComponentsSSO1725
KeywordsSTRUCTURAL GENOMICS
Function / homologyJelly Rolls - #1670 / Cmr7b-like, BtrG-like domain / : / defense response to virus / Jelly Rolls / Sandwich / Mainly Beta / BETA-MERCAPTOETHANOL / Putative CRISPR system CMR subunit Cmr7 2
Function and homology information
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsReeks, J. / Liu, H. / Naismith, J. / White, M. / McMahon, S.
CitationJournal: Mol.Cell / Year: 2012
Title: Structure and Mechanism of the Cmr Complex for Crispr-Mediated Antiviral Immunity.
Authors: Zhang, J. / Rouillon, C. / Kerou, M. / Reeks, J. / Brugger, K. / Graham, S. / Reimann, J. / Cannone, G. / Liu, H. / Albers, S. / Naismith, J.H. / Spagnolo, L. / White, M.F.
History
DepositionOct 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references / Source and taxonomy
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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: SSO1725
B: SSO1725
C: SSO1725
D: SSO1725
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6809
Polymers86,2544
Non-polymers4275
Water2,630146
1
A: SSO1725
B: SSO1725
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2233
Polymers43,1272
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-26.3 kcal/mol
Surface area15970 Å2
MethodPISA
2
C: SSO1725
hetero molecules

D: SSO1725
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4576
Polymers43,1272
Non-polymers3304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1980 Å2
ΔGint-19.9 kcal/mol
Surface area15680 Å2
MethodPISA
3
D: SSO1725
hetero molecules

C: SSO1725
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4576
Polymers43,1272
Non-polymers3304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1980 Å2
ΔGint-19.9 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.750, 90.290, 111.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SSO1725


Mass: 21563.377 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MERCAPTHOETHANOL ADDUCT / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q97XK8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsN-TERMINAL GA COMES FROM TAG. THE S2G MUTATION IS OWING TO THE CLONING STRATEGY USED.

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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: 2.28 Å3/Da / Density % sol: 45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.08→47.48 Å / Num. obs: 46758 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.2
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.08→47.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.609 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. REFMAC NCSR-LOCAL WAS USED FOR NCS RESTRAINTS. BME ADDUCTS ON CYS96 IN A, B, AND C. NOT OBSERVED IN D.
RfactorNum. reflection% reflectionSelection details
Rfree0.23051 2361 5.1 %RANDOM
Rwork0.19906 ---
obs0.20066 44347 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.9 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.08→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 22 146 5977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225936
X-RAY DIFFRACTIONr_bond_other_d0.0060.023934
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.948041
X-RAY DIFFRACTIONr_angle_other_deg1.3593.0019669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40226.027292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.846151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2851516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026537
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021155
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 174 -
Rwork0.275 2795 -
obs--100 %
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)
196.8862-30.8591-7.360510.961-5.613857.6250.20850.7919-0.2385-0.0819-0.67560.16320.2994.66360.46710.1709-0.1471-0.06880.91360.59780.773917.96717.869-2.13
21.93650.63911.3691.06990.40542.624-0.06870.08780.1592-0.13060.03530.1914-0.10260.04090.03340.0307-0.0096-0.01670.017-0.00560.05735.75911.3827.175
34.6411.34211.01692.3895-1.56234.7423-0.09270.42530.1376-0.1750.049-0.0268-0.18680.36070.04370.1703-0.02090.01630.11410.01690.062716.28314.5029.324
43.24541.72463.43321.34841.58314.00160.2923-0.4264-0.02920.1636-0.23680.11930.3272-0.4331-0.05550.0577-0.00960.01140.1027-0.00620.10520.8755.5313.902
54.89471.17410.84722.30240.23825.1175-0.01-0.35080.38140.1475-0.11940.1331-0.32710.02110.12940.0722-0.04310.00290.0657-0.03340.032735.73825.92838.735
62.83320.23621.65881.44390.00043.7143-0.0145-0.25420.11020.1577-0.1417-0.0149-0.15840.030.15620.064-0.0590.01230.081-0.02190.017732.65518.46634.147
73.31360.4431-0.17851.92070.53753.4187-0.0165-0.17440.31730.1406-0.09920.1462-0.2858-0.23620.11570.0813-0.0167-0.00550.0834-0.03750.044625.43222.03530.259
88.76711.21734.07081.6657-0.14946.16050.1566-0.332-0.42560.1482-0.2243-0.180.46950.44710.06770.11190.01330.00980.16840.04010.058343.13516.59734.859
91.1277-0.4366-0.1445.09931.57252.98390.0993-0.11130.05280.0695-0.03480.2546-0.13460.0671-0.06460.0289-0.00150.01880.0441-0.00960.037417.792-11.19720.293
100.3253-1.1112-0.75244.0641.83864.4198-0.08070.0055-0.2540.24890.1150.96750.2363-0.4712-0.03420.0949-0.00570.04150.13780.05550.4317.518-14.50822.298
1112.04777.2162-0.80788.27971.75141.4991-0.0702-0.2145-0.24170.5855-0.11460.04810.47940.020.18470.1860.02060.06280.0736-0.00430.039320.041-24.13222.435
120.095-0.0135-0.26524.74290.98571.63750.03150.0106-0.0463-0.3507-0.0450.0483-0.05590.13860.01350.04990.0344-0.03560.1156-0.02760.083219.798-11.41315.137
132.45460.38891.03824.61651.79254.1673-0.07850.0614-0.2143-0.4664-0.09910.67640.1127-0.53180.17760.1056-0.0503-0.0350.0939-0.01970.265911.01438.582-1.331
142.3645-0.5267-0.31043.30072.33563.9478-0.2078-0.0955-0.244-0.0679-0.00150.42340.0635-0.31420.20930.0434-0.01370.00160.05110.02610.093516.68844.3435.545
155.1648-0.83310.80844.69070.26982.1186-0.20470.28280.0718-0.3761-0.11990.6847-0.1715-0.48160.32460.13370.005-0.09080.2053-0.05330.159510.95851.0832.319
161.4394-0.42990.04914.2872.13913.4071-0.135-0.1489-0.26540.60520.20360.08230.79930.1008-0.06860.22760.03510.03460.03410.04780.135619.80437.5138.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 13
2X-RAY DIFFRACTION2A14 - 116
3X-RAY DIFFRACTION3A117 - 151
4X-RAY DIFFRACTION4A152 - 192
5X-RAY DIFFRACTION5B12 - 47
6X-RAY DIFFRACTION6B48 - 108
7X-RAY DIFFRACTION7B109 - 159
8X-RAY DIFFRACTION8B160 - 192
9X-RAY DIFFRACTION9C12 - 100
10X-RAY DIFFRACTION10C101 - 120
11X-RAY DIFFRACTION11C121 - 134
12X-RAY DIFFRACTION12C135 - 192
13X-RAY DIFFRACTION13D13 - 56
14X-RAY DIFFRACTION14D57 - 109
15X-RAY DIFFRACTION15D110 - 151
16X-RAY DIFFRACTION16D152 - 192

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