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- PDB-2i8e: Structure of SSO1404, a predicted DNA repair-associated protein f... -

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Basic information

Entry
Database: PDB / ID: 2i8e
TitleStructure of SSO1404, a predicted DNA repair-associated protein from Sulfolobus solfataricus P2
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DNA REPAIR / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PSI / Protein Structure Initiative
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
IODIDE ION / CRISPR-associated endoribonuclease Cas2 1
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsWang, S. / Zimmerman, M.D. / Kudritska, M. / Chruszcz, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.
Authors: Beloglazova, N. / Brown, G. / Zimmerman, M.D. / Proudfoot, M. / Makarova, K.S. / Kudritska, M. / Kochinyan, S. / Wang, S. / Chruszcz, M. / Minor, W. / Koonin, E.V. / Edwards, A.M. / Savchenko, A. / Yakunin, A.F.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE, HOWEVER, THAT THIS BIOLOGICAL ASSEMBLY HAS NOT BEEN EXPERIMENTALLY GENERATED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6015
Polymers12,0931
Non-polymers5084
Water1,35175
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,20210
Polymers24,1872
Non-polymers1,0158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area4570 Å2
ΔGint-31 kcal/mol
Surface area9720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.277, 64.277, 39.529
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

DetailsThe biological assembly has not been determined experimentally. The biological unit is predicted by the PITA server (http://http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pita/RunPita.pl) to be a dimer. The second part of the predicted biological assembly is generated by the operation: -x, -y-1, z.

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Components

#1: Protein Hypothetical protein /


Mass: 12093.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: SSO1404 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q97YC2
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallized in 0.2M Na iodide, 20% PEG3350, 2% isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 9, 2006 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. all: 12619 / Num. obs: 12619 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 63.9
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.2 / Num. unique all: 1219 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
ARP/wARPmodel building
RESOLVEphasing
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.59→24.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.102 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22708 610 4.8 %RANDOM
Rwork0.18783 ---
all0.18972 11992 --
obs0.18972 11992 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.59→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 4 75 809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022800
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9791083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50323.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23515159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.091158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02609
X-RAY DIFFRACTIONr_nbd_refined0.2150.2348
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.215
X-RAY DIFFRACTIONr_mcbond_it1.411.5475
X-RAY DIFFRACTIONr_mcangle_it1.6462771
X-RAY DIFFRACTIONr_scbond_it3.273350
X-RAY DIFFRACTIONr_scangle_it4.5714.5310
LS refinement shellResolution: 1.59→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 44 -
Rwork0.159 863 -
obs--99.56 %
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)
12.85240.7170.80841.93151.17392.59460.0195-0.11890.02850.1756-0.07830.0298-0.05-0.02880.0587-0.0427-0.0206-0.0032-0.05010.0017-0.061440.038329.065621.1118
25.13620.5067-1.82232.85792.14426.0271-0.0250.1904-0.18360.0695-0.03460.25460.0691-0.42940.0596-0.0545-0.0259-0.0157-0.00530.016-0.030132.547724.938718.6142
34.2336-1.86443.70593.2354-2.80886.24880.08020.2398-0.0898-0.038-0.08120.09870.03240.12810.0009-0.0769-0.0158-0.0027-0.02330.0003-0.055437.657525.324813.8866
42.5881-0.2632-0.22031.98484.055613.1211-0.0283-0.12220.3808-0.003-0.120.0572-0.2025-0.21070.1484-0.00190.00960.0022-0.0128-0.0032-0.021932.972636.785118.4578
51.37451.25142.63531.48952.06295.37590.0798-0.11660.15350.0472-0.0971-0.0315-0.0923-0.15520.0174-0.0217-0.0106-0.00760.008-0.0125-0.025343.725236.39224.5366
65.2431-2.28527.02563.3656-4.324713.86640.0410.1135-0.42090.02890.04640.08610.2813-0.0548-0.08740.01870.0155-0.0043-0.0198-0.0397-0.016950.962618.433710.7894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 192 - 19
2X-RAY DIFFRACTION2AA20 - 3020 - 30
3X-RAY DIFFRACTION3AA31 - 4631 - 46
4X-RAY DIFFRACTION4AA47 - 5847 - 58
5X-RAY DIFFRACTION5AA59 - 7559 - 75
6X-RAY DIFFRACTION6AA76 - 8976 - 89

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