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- PDB-4p80: Structure of ancestral PyrR protein (AncGREENPyrR) -

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Basic information

Entry
Database: PDB / ID: 4p80
TitleStructure of ancestral PyrR protein (AncGREENPyrR)
ComponentsAncestral PyrR protein (Green)
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 / Resolution: 1.6 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 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral PyrR protein (Green)
B: Ancestral PyrR protein (Green)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4856
Polymers40,1002
Non-polymers3844
Water5,927329
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-65 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.430, 67.030, 56.820
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ancestral PyrR protein (Green)


Mass: 20050.131 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 1.2M Ammonium Sulfate, 0.08M Na acetate pH4.8, 20% Glycerol

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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 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→20.27 Å / Num. obs: 54426 / % possible obs: 95.4 % / Redundancy: 2.9 % / Net I/σ(I): 5.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementResolution: 1.6→60.57 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.897 / SU B: 1.861 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24804 2766 4.8 %RANDOM
Rwork0.21467 ---
obs0.21623 54426 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.51 Å2
2---0.41 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.6→60.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 20 329 2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192701
X-RAY DIFFRACTIONr_bond_other_d0.0010.022768
X-RAY DIFFRACTIONr_angle_refined_deg2.2451.9973664
X-RAY DIFFRACTIONr_angle_other_deg0.9836367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48924.386114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81215532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3721526
X-RAY DIFFRACTIONr_chiral_restr0.1410.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02541
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_it1.3060.7621374
X-RAY DIFFRACTIONr_mcbond_other1.30.7611373
X-RAY DIFFRACTIONr_mcangle_it2.051.1291732
X-RAY DIFFRACTIONr_mcangle_other2.0511.1311733
X-RAY DIFFRACTIONr_scbond_it2.2171.0111327
X-RAY DIFFRACTIONr_scbond_other2.2051.0091311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4311.4231907
X-RAY DIFFRACTIONr_long_range_B_refined5.0227.6211392
X-RAY DIFFRACTIONr_long_range_B_other4.8257.27611090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 232 -
Rwork0.251 4026 -
obs--96.84 %

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