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- PDB-4p3k: Structure of ancestral PyrR protein (PLUMPyrR) -

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Basic information

Entry
Database: PDB / ID: 4p3k
TitleStructure of ancestral PyrR protein (PLUMPyrR)
ComponentsAncestral PyrR protein (Plum)
KeywordsUNKNOWN FUNCTION / RNA binding proteins / reconstructed amino acid sequence
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPerica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
CitationJournal: Science / Year: 2014
Title: Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Authors: Perica, T. / Kondo, Y. / Tiwari, S.P. / McLaughlin, S.H. / Kemplen, K.R. / Zhang, X. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
History
DepositionMar 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Dec 27, 2023Group: 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 / citation / database_2 / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Ancestral PyrR protein (Plum)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5365
Polymers20,0821
Non-polymers4534
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.960, 57.240, 54.000
Angle α, β, γ (deg.)90.00, 127.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

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Components

#1: Protein Ancestral PyrR protein (Plum)


Mass: 20082.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Bacteria (eubacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 40% PEG-300, 0.1M Tris pH 7.0, 5% PEG-1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→42.86 Å / Num. obs: 20089 / % possible obs: 99 % / Redundancy: 6.7 % / Net I/σ(I): 11.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.199 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1023 5.1 %RANDOM
Rwork0.16425 ---
obs0.16669 19065 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.516 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20.42 Å2
2---1.11 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 27 137 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021467
X-RAY DIFFRACTIONr_angle_refined_deg1.942.0081932
X-RAY DIFFRACTIONr_angle_other_deg0.92833371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44823.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91215274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
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_it2.9662.284711
X-RAY DIFFRACTIONr_mcbond_other2.9552.276710
X-RAY DIFFRACTIONr_mcangle_it4.5813.399887
X-RAY DIFFRACTIONr_mcangle_other4.5793.406888
X-RAY DIFFRACTIONr_scbond_it4.6483.132721
X-RAY DIFFRACTIONr_scbond_other4.6473.133721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3824.3931046
X-RAY DIFFRACTIONr_long_range_B_refined9.74223.4495877
X-RAY DIFFRACTIONr_long_range_B_other9.74223.455877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 68 -
Rwork0.241 1421 -
obs--99.47 %

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