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- PDB-4p86: Structure of PyrR protein from Bacillus subtilis with GMP -

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Basic information

Entry
Database: PDB / ID: 4p86
TitleStructure of PyrR protein from Bacillus subtilis with GMP
ComponentsBifunctional protein PyrR
KeywordsTRANSFERASE / RNA binding proteins
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-MONOPHOSPHATE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: Bifunctional protein PyrR
B: Bifunctional protein PyrR
C: Bifunctional protein PyrR
D: Bifunctional protein PyrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,00111
Polymers81,7304
Non-polymers2,2717
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-20 kcal/mol
Surface area30310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.940, 77.530, 99.780
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14C
24B
15C
25D
16B
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASNAA3 - 1804 - 181
21GLNGLNASNASNCC3 - 1804 - 181
12LYSLYSGLUGLUAA4 - 1815 - 182
22LYSLYSGLUGLUBB4 - 1815 - 182
13GLNGLNASNASNAA3 - 1804 - 181
23GLNGLNASNASNDD3 - 1804 - 181
14LYSLYSGLUGLUCC4 - 1795 - 180
24LYSLYSGLUGLUBB4 - 1795 - 180
15GLNGLNASNASNCC3 - 1804 - 181
25GLNGLNASNASNDD3 - 1804 - 181
16LYSLYSGLUGLUBB4 - 1795 - 180
26LYSLYSGLUGLUDD4 - 1795 - 180

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 20432.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pRSET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25.5% PEG 4000, 0.085 M Na Citrate pH 5.6, 0.17 M Ammonium Acetate, 15% Glycerol

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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: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→54.58 Å / Num. obs: 50228 / % possible obs: 96.4 % / Redundancy: 2.7 % / Net I/σ(I): 10.9
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3c

1a3c


Resolution: 1.93→54.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.087 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 2692 5.1 %RANDOM
Rwork0.17959 ---
obs0.18136 50228 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.056 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-1.31 Å2
2--1.45 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.93→54.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 150 203 5830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195698
X-RAY DIFFRACTIONr_bond_other_d0.0110.025662
X-RAY DIFFRACTIONr_angle_refined_deg1.9952.027733
X-RAY DIFFRACTIONr_angle_other_deg1.759312994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08624.656262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.206151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3241556
X-RAY DIFFRACTIONr_chiral_restr0.120.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026284
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021160
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_it4.6234.1152797
X-RAY DIFFRACTIONr_mcbond_other4.6214.1132796
X-RAY DIFFRACTIONr_mcangle_it6.5336.1163484
X-RAY DIFFRACTIONr_mcangle_other6.5326.1193485
X-RAY DIFFRACTIONr_scbond_it5.9434.8122901
X-RAY DIFFRACTIONr_scbond_other5.9414.8122901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7946.9624250
X-RAY DIFFRACTIONr_long_range_B_refined11.87839.83523543
X-RAY DIFFRACTIONr_long_range_B_other11.87839.83523543
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)
11A104590.15
12C104590.15
21A106510.14
22B106510.14
31A110550.13
32D110550.13
41C103630.14
42B103630.14
51C103940.16
52D103940.16
61B105630.14
62D105630.14
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 188 -
Rwork0.275 3730 -
obs--96.74 %

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