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- PDB-4p84: Structure of engineered PyrR protein (VIOLET PyrR) -

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Basic information

Entry
Database: PDB / ID: 4p84
TitleStructure of engineered PyrR protein (VIOLET PyrR)
ComponentsBifunctional protein PyrR
KeywordsTRANSFERASE / 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: 2.2 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 30, 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 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Bifunctional protein PyrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5005
Polymers20,1241
Non-polymers3764
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-24 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 56.400, 60.165
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-368-

HOH

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Components

#1: Protein Bifunctional protein PyrR / PYRIMIDINE OPERON REGULATORY PROTEIN PYRR


Mass: 20123.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: uracil phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG-600, 10% glycerol, 0.1M Tris pH 7.0, 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→42.55 Å / Num. obs: 8535 / % possible obs: 98.4 % / Redundancy: 2.6 % / Net I/σ(I): 3.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3c

1a3c


Resolution: 2.2→42.55 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.863 / SU B: 8.39 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 434 4.8 %RANDOM
Rwork0.20466 ---
obs0.20767 8535 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.186 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å21.39 Å2
2--1.44 Å20 Å2
3----3.18 Å2
Refinement stepCycle: 1 / Resolution: 2.2→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 22 154 1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191460
X-RAY DIFFRACTIONr_bond_other_d0.0020.021472
X-RAY DIFFRACTIONr_angle_refined_deg1.7682.0051978
X-RAY DIFFRACTIONr_angle_other_deg0.81433380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96424.17967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2291516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
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_it1.8292.255729
X-RAY DIFFRACTIONr_mcbond_other1.8072.25728
X-RAY DIFFRACTIONr_mcangle_it2.9113.359913
X-RAY DIFFRACTIONr_mcangle_other2.9113.365914
X-RAY DIFFRACTIONr_scbond_it2.4842.647728
X-RAY DIFFRACTIONr_scbond_other2.4812.647728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1143.8291065
X-RAY DIFFRACTIONr_long_range_B_refined7.12121.7156353
X-RAY DIFFRACTIONr_long_range_B_other7.12221.7146353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 41 -
Rwork0.209 621 -
obs--97.35 %

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