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- PDB-6tif: ReoM- Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 6tif
TitleReoM- Listeria monocytogenes
ComponentsUPF0297 protein lmo1503
KeywordsCELL CYCLE / 5-helical bundle / dimer / Listeria monocytogenes / phosphoprotein
Function / homologyIreB regulatory phosphoprotein / IreB regulatory phosphoprotein / UPF0297 protein lmo1503
Function and homology information
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRutter, Z.J. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011186/1 United Kingdom
CitationJournal: Elife / Year: 2020
Title: PrkA controls peptidoglycan biosynthesis through the essential phosphorylation of ReoM.
Authors: Wamp, S. / Rutter, Z.J. / Rismondo, J. / Jennings, C.E. / Moller, L. / Lewis, R.J. / Halbedel, S.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 2.0Jun 22, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_ref_seq.pdbx_strand_id
Revision 2.1Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: UPF0297 protein lmo1503
A: UPF0297 protein lmo1503
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5026
Polymers21,1182
Non-polymers3844
Water1,69394
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-79 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.788, 58.619, 74.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0297 protein lmo1503


Mass: 10558.985 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo1503 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60357
#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.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate/citrate 0.2 lithium sulphate 20 % w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→74.45 Å / Num. obs: 23059 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.986 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1129 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5US5

5us5


Resolution: 1.6→37.252 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.961 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2137 960 4.172 %
Rwork0.153 --
all0.156 --
obs-23008 99.731 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.171 Å2
Baniso -1Baniso -2Baniso -3
1-1.516 Å20 Å2-0 Å2
2---2.119 Å20 Å2
3---0.603 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 20 94 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131438
X-RAY DIFFRACTIONr_bond_other_d0.0060.0171343
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6481935
X-RAY DIFFRACTIONr_angle_other_deg1.4581.593123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88723.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7851510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02286
X-RAY DIFFRACTIONr_nbd_refined0.2270.2314
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21188
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2697
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.225
X-RAY DIFFRACTIONr_nbd_other0.2360.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.222
X-RAY DIFFRACTIONr_mcbond_it4.3862.185682
X-RAY DIFFRACTIONr_mcbond_other4.3722.184682
X-RAY DIFFRACTIONr_mcangle_it5.0823.292850
X-RAY DIFFRACTIONr_mcangle_other5.0823.297851
X-RAY DIFFRACTIONr_scbond_it5.0182.874756
X-RAY DIFFRACTIONr_scbond_other4.7422.831741
X-RAY DIFFRACTIONr_scangle_it6.2244.0561084
X-RAY DIFFRACTIONr_scangle_other5.6993.9841061
X-RAY DIFFRACTIONr_lrange_it6.15226.6851636
X-RAY DIFFRACTIONr_lrange_other6.11726.4691625
X-RAY DIFFRACTIONr_rigid_bond_restr3.60932781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.231657X-RAY DIFFRACTION99.7592
1.642-1.6870.237130.2071636X-RAY DIFFRACTION99.4572
1.687-1.7350.292730.191503X-RAY DIFFRACTION99.8733
1.735-1.7890.268810.1691454X-RAY DIFFRACTION99.6106
1.789-1.8480.251620.1611438X-RAY DIFFRACTION99.6678
1.848-1.9120.192760.1561370X-RAY DIFFRACTION99.8619
1.912-1.9840.246730.1491317X-RAY DIFFRACTION99.5702
1.984-2.0650.203730.1231298X-RAY DIFFRACTION99.7817
2.065-2.1570.234600.121239X-RAY DIFFRACTION99.8463
2.157-2.2620.223480.1421202X-RAY DIFFRACTION99.8403
2.262-2.3850.212510.1241122X-RAY DIFFRACTION99.7449
2.385-2.5290.204570.1231069X-RAY DIFFRACTION99.646
2.529-2.7040.202470.1281026X-RAY DIFFRACTION99.7212
2.704-2.920.232580.151926X-RAY DIFFRACTION99.696
2.92-3.1980.195420.147885X-RAY DIFFRACTION99.7847
3.198-3.5750.174340.152798X-RAY DIFFRACTION100
3.575-4.1260.183380.144714X-RAY DIFFRACTION99.4709
4.126-5.0490.204420.141601X-RAY DIFFRACTION100
5.049-7.1250.271230.214490X-RAY DIFFRACTION100

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