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- PDB-2w0m: Crystal Structure of sso2452 from Sulfolobus solfataricus P2 -

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Basic information

Entry
Database: PDB / ID: 2w0m
TitleCrystal Structure of sso2452 from Sulfolobus solfataricus P2
ComponentsSSO2452
KeywordsUNKNOWN FUNCTION / SSO2452 / RECA / SULFOLOBUS SOLFATARICUS P2 / SSPF
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
KaiC-related / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / KaiC domain-containing protein
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcRobbie, A. / Carter, L. / Johnson, K.A. / Kerou, M. / Liu, H. / Mcmahon, S. / Oke, M. / Naismith, J.H. / White, M.F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and Functional Characterisation of a Conserved Archaeal Rada Paralog with Antirecombinase Activity.
Authors: Mcrobbie, A.M. / Carter, L.G. / Kerou, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Oke, M. / Naismith, J.H. / White, M.F.
History
DepositionAug 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 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_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: SSO2452
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4796
Polymers27,0411
Non-polymers4385
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.105, 169.596, 39.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SSO2452


Mass: 27041.307 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS P2 (archaea) / Plasmid: PDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97VZ8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.26 Å3/Da / Density % sol: 45.64 % / Description: NONE
Crystal growpH: 5.5 / Details: PEG 8K 8.94% , MES 0.1M PH 5.5, ZN-ACETATE 0.15M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 14, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 19173 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.62
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.31 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DR3

2dr3


Resolution: 2→29.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.175 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 983 5.1 %RANDOM
Rwork0.20049 ---
obs0.20294 18190 98.36 %-
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: 29.126 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 13 98 1892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221828
X-RAY DIFFRACTIONr_bond_other_d00.021281
X-RAY DIFFRACTIONr_angle_refined_deg1.0171.9642462
X-RAY DIFFRACTIONr_angle_other_deg0.65933112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19523.64785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3121514
X-RAY DIFFRACTIONr_chiral_restr0.060.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
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_it0.4351.51090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84621763
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2973738
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2354.5698
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→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.436 75
Rwork0.264 1353
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)
12.2217-1.0684-0.3583.44390.99075.1146-0.0304-0.3091-0.04830.35980.0640.05240.2390.0713-0.0336-0.1679-0.0192-0.03-0.18690.0013-0.164535.53925.94844.246
24.2235-0.79370.41013.65830.9563.01640.04160.08760.1515-0.103-0.12530.3962-0.2379-0.33730.0837-0.20930.01730.0099-0.18590.0074-0.093725.51534.68338.069
32.6792-1.27520.20346.5325-1.28483.55380.06420.1618-0.5569-0.2697-0.05610.23820.35460.1097-0.0081-0.10880.0352-0.0214-0.1452-0.0399-0.035437.91415.15730.923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1240
3X-RAY DIFFRACTION2A102 - 164
4X-RAY DIFFRACTION3A165 - 235
5X-RAY DIFFRACTION3A1236 - 1237
6X-RAY DIFFRACTION3A1239

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