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- PDB-2ivy: Crystal structure of hypothetical protein sso1404 from Sulfolobus... -

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Basic information

Entry
Database: PDB / ID: 2ivy
TitleCrystal structure of hypothetical protein sso1404 from Sulfolobus solfataricus P2
ComponentsHYPOTHETICAL PROTEIN SSO1404
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / CAS / RNAI / CRISPR
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2 1
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsYan, X. / Carter, L.G. / Dorward, M. / Liu, H. / McMahon, S.A. / Oke, M. / Powers, H. / White, M.F. / Naismith, J.H.
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
DepositionJun 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: HYPOTHETICAL PROTEIN SSO1404


Theoretical massNumber of molelcules
Total (without water)11,8791
Polymers11,8791
Non-polymers00
Water1,892105
1
A: HYPOTHETICAL PROTEIN SSO1404

A: HYPOTHETICAL PROTEIN SSO1404


Theoretical massNumber of molelcules
Total (without water)23,7572
Polymers23,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area3670 Å2
ΔGint-26.4 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.493, 64.493, 39.219
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-8-

PHE

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Components

#1: Protein HYPOTHETICAL PROTEIN SSO1404


Mass: 11878.636 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q97YC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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 Å3/Da / Density % sol: 38 %
Crystal growpH: 7 / Details: 30% PEG 1000, 0.1M TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 18390 / % possible obs: 99.7 % / Observed criterion σ(I): 6 / Redundancy: 10.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZPW

1zpw


Resolution: 1.4→18.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.845 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 90-101 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 941 5.1 %RANDOM
Rwork0.164 ---
obs0.165 17425 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→18.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 0 105 835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.98996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.356589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20223.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51515148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.592158
X-RAY DIFFRACTIONr_chiral_restr0.090.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2322
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2531
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3111.5452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7842708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5823324
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7724.5287
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: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 82
Rwork0.207 1255
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)
112.33081.819-0.20718.456-0.022811.74440.1429-0.641-0.0960.563-0.20820.07250.2611-0.13460.06520.0606-0.0454-0.00910.0785-0.01280.040143.79320.916-2.97
23.1780.5339-0.73732.13270.19882.4584-0.05060.5216-0.1392-0.27520.0564-0.01380.179-0.1479-0.00580.0239-0.0137-0.00120.10550.00030.01145.93119.838-22.952
34.58030.6164-1.90958.637-0.29738.57570.03420.19460.0027-0.13660.07790.18030.2554-0.2633-0.11210.0557-0.0216-0.02070.05580.00310.043940.21715.254-18.007
45.43322.7461-0.922125.66442.20410.79220.0809-0.0018-0.07270.4534-0.30510.33210.6869-0.32530.22420.0638-0.04880.00640.13040.02850.106336.0616.304-12.86
51.2151-0.2730.56763.6499-2.2664.24840.0198-0.0188-0.00820.1734-0.06520.11060.0274-0.01230.04540.0399-0.0285-0.00020.07590.00730.072240.92120.045-10.411
63.72450.488-4.6435.1586-0.668411.9956-0.156-0.184-0.25480.07310.0063-0.34220.26210.35150.14970.053-0.0088-0.00560.04610.00520.055948.38910.257-14.622
79.25056.9501-15.068521.359-13.799724.9265-1.2120.8356-0.3831-1.28631.01840.56261.5175-1.37870.19360.0699-0.07620.01040.1237-0.03240.054656.26414.56-29.311
83.28030.226-4.88970.208-0.459511.32860.11350.06160.0795-0.01830.0564-0.0802-0.13290.0709-0.16990.0326-0.00880.00440.03970.00250.056152.36721.963-17.705
914.6112-7.37010.602616.0702-4.51228.50620.0189-0.55760.03010.37550.24510.60760.0381-0.3827-0.2640.0501-0.01180.06060.0937-0.01220.048941.15330.456-0.698
103.6376-0.42221.54145.8643-9.87324.92610.00520.07290.22940.1196-0.0650.2472-0.5243-0.0720.05980.06770.03060.01110.0499-0.01560.07942.14838.59-12.842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 6
2X-RAY DIFFRACTION2A7 - 19
3X-RAY DIFFRACTION3A20 - 24
4X-RAY DIFFRACTION4A25 - 30
5X-RAY DIFFRACTION5A31 - 46
6X-RAY DIFFRACTION6A47 - 58
7X-RAY DIFFRACTION7A59 - 63
8X-RAY DIFFRACTION8A64 - 75
9X-RAY DIFFRACTION9A76 - 81
10X-RAY DIFFRACTION10A82 - 89

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