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- PDB-4p83: Structure of engineered PyrR protein (PURPLE PyrR) -

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Basic information

Entry
Database: PDB / ID: 4p83
TitleStructure of engineered PyrR protein (PURPLE PyrR)
ComponentsEngineered PyrR protein (Purple)
KeywordsTRANSCRIPTION / RNA binding proteins / reconstructed amino acid sequence
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / URIDINE-5'-MONOPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Engineered PyrR protein (Purple)
B: Engineered PyrR protein (Purple)
C: Engineered PyrR protein (Purple)
D: Engineered PyrR protein (Purple)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4218
Polymers81,1254
Non-polymers1,2974
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-30 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.150, 77.150, 286.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA5 - 1805 - 180
21GLUGLUBB5 - 1805 - 180
12GLUGLUAA5 - 1805 - 180
22GLUGLUCC5 - 1805 - 180
13GLUGLUAA5 - 1805 - 180
23GLUGLUDD5 - 1805 - 180
14ASNASNBB5 - 1815 - 181
24ASNASNCC5 - 1815 - 181
15ASNASNBB5 - 1815 - 181
25ASNASNDD5 - 1815 - 181
16ASNASNCC5 - 1815 - 181
26ASNASNDD5 - 1815 - 181

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Engineered PyrR protein (Purple)


Mass: 20281.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Bacteria (eubacteria)
#2: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Magnesium Chloride

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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 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→53.59 Å / Num. obs: 29162 / % possible obs: 99 % / Redundancy: 11.9 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.166 / Mean I/σ(I) obs: 2.4

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Processing

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

1a3c


Resolution: 2.5→74.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.453 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25122 1546 5 %RANDOM
Rwork0.20159 ---
obs0.20401 29162 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.048 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0 Å2-0 Å2
2--1.83 Å2-0 Å2
3----3.66 Å2
Refinement stepCycle: 1 / Resolution: 2.5→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 84 134 5468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195404
X-RAY DIFFRACTIONr_bond_other_d0.0120.025427
X-RAY DIFFRACTIONr_angle_refined_deg1.86727328
X-RAY DIFFRACTIONr_angle_other_deg1.84312411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83323.295258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.77815970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0821571
X-RAY DIFFRACTIONr_chiral_restr0.0920.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215993
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021150
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_it3.9534.7382680
X-RAY DIFFRACTIONr_mcbond_other3.9514.7372679
X-RAY DIFFRACTIONr_mcangle_it6.1667.0733336
X-RAY DIFFRACTIONr_mcangle_other6.1667.0743337
X-RAY DIFFRACTIONr_scbond_it4.5165.32724
X-RAY DIFFRACTIONr_scbond_other4.5165.3012723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0527.7463993
X-RAY DIFFRACTIONr_long_range_B_refined10.78244.84921808
X-RAY DIFFRACTIONr_long_range_B_other10.78144.84921809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98250.16
12B98250.16
21A97610.15
22C97610.15
31A99810.14
32D99810.14
41B97880.16
42C97880.16
51B99800.16
52D99800.16
61C101330.15
62D101330.15
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 117 -
Rwork0.279 2111 -
obs--99.42 %

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