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- PDB-2x5q: Crystal Structure of Hypothetical protein sso1986 from Sulfolobus... -

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Basic information

Entry
Database: PDB / ID: 2x5q
TitleCrystal Structure of Hypothetical protein sso1986 from Sulfolobus solfataricus P2
ComponentsSSO1986
KeywordsUNKNOWN FUNCTION
Function / homologyCRISPR system CMR subunit Cmr7 1 / CRISPR system CMR subunit Cmr7 1 / : / CRISPR-cas system / defense response to virus / cytoplasm / CRISPR system CMR subunit Cmr7 1
Function and homology information
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOke, M. / Carter, L. / Johnson, K.A. / Kerou, M. / Liu, H. / Mcmahon, S. / Naismith, J.H. / White, M.F.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SSO1986
B: SSO1986


Theoretical massNumber of molelcules
Total (without water)44,4702
Polymers44,4702
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-15.8 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.933, 46.183, 62.574
Angle α, β, γ (deg.)90.00, 109.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2050-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A7 - 123
2115B7 - 123
1125A132 - 193
2125B132 - 193

NCS ensembles :
ID
1
2

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Components

#1: Protein SSO1986


Mass: 22235.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97WX5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.97 Å3/Da / Density % sol: 37.41 % / Description: NONE
Crystal growpH: 4
Details: 19.2% PEG 6000, 0.1M NA-CITRATE, PH4.0, 0.93M LICL2, 9% ETHYLENE GLYCOL FREEZING SOLUTION: 21.0% PEG 6000, 0.1M NA-CITRATE, PH4.0, 0.5M LICL2, 25% ETHYLENE GLYCOL.DERIVATIVE CRYSTALS FOR SAD ...Details: 19.2% PEG 6000, 0.1M NA-CITRATE, PH4.0, 0.93M LICL2, 9% ETHYLENE GLYCOL FREEZING SOLUTION: 21.0% PEG 6000, 0.1M NA-CITRATE, PH4.0, 0.5M LICL2, 25% ETHYLENE GLYCOL.DERIVATIVE CRYSTALS FOR SAD PHASING WERE OBTAINED BY SOAKING THE CRYSTALS IN 200 MM TRIMETHYLLEAD CHLORIDE, 500 MM POTASSIUM OSMATE AND 200 MM DIPOTASSIUM HEXACHLORO OSMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.05→29.54 Å / Num. obs: 20562 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 4.5
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.05→29.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.469 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22682 1085 5 %RANDOM
Rwork0.18883 ---
obs0.19073 20562 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.249 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20.55 Å2
2--1.84 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 0 190 3096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222969
X-RAY DIFFRACTIONr_bond_other_d0.0010.021999
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9614014
X-RAY DIFFRACTIONr_angle_other_deg0.82434935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25225.87138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77715558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.29158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.2050.2533
X-RAY DIFFRACTIONr_nbd_other0.1850.21982
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21457
X-RAY DIFFRACTIONr_nbtor_other0.0830.21599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.52421
X-RAY DIFFRACTIONr_mcbond_other0.1281.5736
X-RAY DIFFRACTIONr_mcangle_it0.84722953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4131454
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8294.51059
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A678medium positional0.150.5
12B678medium positional0.150.5
21A364medium positional0.20.5
22B364medium positional0.20.5
11A835loose positional0.525
12B835loose positional0.525
21A487loose positional0.735
22B487loose positional0.735
11A678medium thermal0.522
12B678medium thermal0.522
21A364medium thermal0.472
22B364medium thermal0.472
11A835loose thermal0.8910
12B835loose thermal0.8910
21A487loose thermal0.7710
22B487loose thermal0.7710
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 78 -
Rwork0.206 1443 -
obs--94.12 %
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)
13.21860.8939-0.39882.79570.16761.8462-0.040.1753-0.0588-0.15020.00970.10340.1144-0.10290.0303-0.118-0.0047-0.0035-0.1238-0.0209-0.161425.931411.482312.7292
22.85580.92810.93631.9741-0.01342.1289-0.03250.2410.1242-0.2015-0.0178-0.0105-0.10280.10890.0503-0.1239-0.0021-0.002-0.12450.0023-0.169855.342516.563413.5962
34.45252.8048-0.68272.7579-0.76561.08050.2815-0.14420.73660.2582-0.10450.5103-0.1941-0.0513-0.1771-0.0491-0.00170.0244-0.1129-0.0573-0.01720.3721.148417.7903
45.35292.63451.98491.85131.05961.24070.15450.0463-0.5520.092-0.0142-0.20750.19260.0607-0.1403-0.08370.03090.0084-0.1386-0.0223-0.105760.54219.480620.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 124
2X-RAY DIFFRACTION2B7 - 123
3X-RAY DIFFRACTION3A132 - 196
4X-RAY DIFFRACTION4B130 - 196

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