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- PDB-4wyh: Crystal structure of PriX from the hyperthermophilic archaeon Sul... -

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Basic information

Entry
Database: PDB / ID: 4wyh
TitleCrystal structure of PriX from the hyperthermophilic archaeon Sulfolobus solfataricus
ComponentsUncharacterized protein
KeywordsREPLICATION / A novel noncatalytic subunit archaeal eukaryal-type primase
Function / homologyPrimase X / Primase X / metal ion binding / IODIDE ION / Primase X domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsOuyang, S.
CitationJournal: Nat Commun / Year: 2015
Title: A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase.
Authors: Liu, B. / Ouyang, S. / Makarova, K.S. / Xia, Q. / Zhu, Y. / Li, Z. / Guo, L. / Koonin, E.V. / Liu, Z.J. / Huang, L.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7656
Polymers15,1301
Non-polymers6355
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.258, 36.232, 83.758
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 Uncharacterized protein


Mass: 15130.359 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0502 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZS7
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M potassium iodide, 20% (w/v) polyethylene glycol 3,350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→23.424 Å / Num. obs: 6218 / % possible obs: 92.81 % / Redundancy: 11.8 % / Net I/σ(I): 105.56

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→23.424 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1801 615 9.89 %Random
Rwork0.1577 ---
obs0.1598 6218 92.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→23.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 5 87 927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019850
X-RAY DIFFRACTIONf_angle_d1.7331139
X-RAY DIFFRACTIONf_dihedral_angle_d14.317331
X-RAY DIFFRACTIONf_chiral_restr0.118122
X-RAY DIFFRACTIONf_plane_restr0.009139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9503-2.14640.19961230.1491107X-RAY DIFFRACTION75
2.1464-2.45670.16551640.15491429X-RAY DIFFRACTION98
2.4567-3.09410.18141640.16241503X-RAY DIFFRACTION99
3.0941-23.4260.18131640.15861564X-RAY DIFFRACTION98

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