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- PDB-5fbu: Crystal structure of rifampin phosphotransferase RPH-Lm from List... -

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Basic information

Entry
Database: PDB / ID: 5fbu
TitleCrystal structure of rifampin phosphotransferase RPH-Lm from Listeria monocytogenes in complex with rifampin-phosphate
ComponentsPhosphoenolpyruvate synthase
KeywordsTRANSFERASE/ANTIBIOTIC / antibiotic resistance / rifamycins / rifampin / phosphotransferase / ATP grasp domain / phosphohistidine domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


kinase activity / phosphorylation / ATP binding
Similarity search - Function
Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Rifampin-phosphate / Phosphoenolpyruvate synthase
Similarity search - Component
Biological speciesListeria monocytogenes serotype 4b str. F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Skarina, T. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Nat Commun / Year: 2016
Title: Rifampin phosphotransferase is an unusual antibiotic resistance kinase.
Authors: Stogios, P.J. / Cox, G. / Spanogiannopoulos, P. / Pillon, M.C. / Waglechner, N. / Skarina, T. / Koteva, K. / Guarne, A. / Savchenko, A. / Wright, G.D.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Structure summary
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0424
Polymers96,9921
Non-polymers1,0513
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-14 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.630, 151.630, 191.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-902-

CL

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Components

#1: Protein Phosphoenolpyruvate synthase


Mass: 96991.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 4b str. F2365 (bacteria)
Gene: LmNIHS28_01948 / Plasmid: pMCSG53 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0X1KHF9*PLUS
#2: Chemical ChemComp-5WP / Rifampin-phosphate


Mass: 897.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H69N4O14P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence matches to NCBI WP_010958733 but it is not available in UNP database yet.

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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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 mM rifampin, 5 mM ATP, 35% tacsimate, 10 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→49.63 Å / Num. obs: 30989 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FBT

5fbt


Resolution: 2.85→49.633 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2942 1463 4.73 %Random selection
Rwork0.2378 ---
obs0.2405 30933 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→49.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 71 167 5680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075597
X-RAY DIFFRACTIONf_angle_d1.3417592
X-RAY DIFFRACTIONf_dihedral_angle_d16.5162079
X-RAY DIFFRACTIONf_chiral_restr0.064874
X-RAY DIFFRACTIONf_plane_restr0.009980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.95190.39511330.32322885X-RAY DIFFRACTION100
2.9519-3.07010.35471490.28982876X-RAY DIFFRACTION100
3.0701-3.20980.35491560.28552891X-RAY DIFFRACTION100
3.2098-3.3790.32991500.26692892X-RAY DIFFRACTION100
3.379-3.59060.35961450.25122914X-RAY DIFFRACTION100
3.5906-3.86770.28291340.22572934X-RAY DIFFRACTION100
3.8677-4.25680.23351350.21112940X-RAY DIFFRACTION100
4.2568-4.87230.25551630.19662957X-RAY DIFFRACTION100
4.8723-6.13670.30141360.23743017X-RAY DIFFRACTION100
6.1367-49.64010.27681620.23713164X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4019-3.35643.88938.7974-0.1414.10430.0302-0.96060.18111.29450.15490.86871.05652.01030.01281.29940.1118-0.04811.7810.07631.1721-59.1797-43.3244-17.8078
25.1741.5978-0.16076.8966-4.19249.2689-1.0399-0.2849-0.2558-0.4433-0.17470.67360.57130.27461.31611.23070.23470.00061.2350.11051.4862-58.0753-64.0775-18.4592
31.3474-0.2165-1.01014.46470.48645.61880.52550.6317-0.221-2.0378-0.1011-0.0860.216-0.3942-0.27111.92720.5676-0.41630.6375-0.19891.1499-39.2979-35.4613-22.7884
41.4982-0.5535-0.27923.2314-0.4492.35740.2280.56730.4687-0.5928-0.2183-0.1512-0.94450.10750.15030.59520.23020.0337-0.00930.16231.0629-23.7558-28.74230.8091
52.02050.062-0.33771.66110.33951.16350.0045-0.3726-0.01860.0871-0.0270.0056-0.0840.0720.01270.26970.00690.03870.21360.03550.6186-15.4289-44.571720.0477
63.5709-1.0618-0.25681.47790.75121.39950.05060.3464-0.0518-0.3353-0.0418-0.0955-0.14610.07220.01490.3246-0.04610.07230.1880.00670.5974-13.2845-46.8247-0.3036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:35)
2X-RAY DIFFRACTION2(chain A and resid 36:178)
3X-RAY DIFFRACTION3(chain A and resid 179:309)
4X-RAY DIFFRACTION4(chain A and resid 310:430)
5X-RAY DIFFRACTION5(chain A and resid 431:723)
6X-RAY DIFFRACTION6(chain A and resid 724:867)

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