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

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Basic information

Entry
Database: PDB / ID: 5fbs
TitleCrystal structure of rifampin phosphotransferase RPH-Lm from Listeria monocytogenes in complex with ADP and magnesium
ComponentsPhosphoenolpyruvate synthase
KeywordsTRANSFERASE / antibiotic resistance / rifamycins / rifampin / phosphotransferase / ATP grasp domain / phosphohistidine domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPhosphohistidine domain / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesListeria monocytogenes serotype 4b str. F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 1.0Jan 13, 2016Provider: 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

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Assembly

Deposited unit
A: Phosphoenolpyruvate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4433
Polymers96,9921
Non-polymers4522
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-13 kcal/mol
Surface area38990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.510, 58.510, 601.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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)
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence matches to NCBI WP_010958733 which 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5 mM ADP, 20% PEG3350, 0.2 M calcium chloride, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.59→50.54 Å / Num. obs: 34559 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.3
Reflection shellResolution: 2.59→2.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FBT

5fbt


Resolution: 2.59→50.54 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3177 1722 5 %Random selection
Rwork0.2604 ---
obs0.2634 34559 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6161 0 28 49 6238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066291
X-RAY DIFFRACTIONf_angle_d1.1618507
X-RAY DIFFRACTIONf_dihedral_angle_d14.9472370
X-RAY DIFFRACTIONf_chiral_restr0.058983
X-RAY DIFFRACTIONf_plane_restr0.0051084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5901-2.63050.38721410.35792674X-RAY DIFFRACTION100
2.6305-2.67370.42231430.35672764X-RAY DIFFRACTION100
2.6737-2.71980.46921380.35542603X-RAY DIFFRACTION100
2.7198-2.76920.43131490.35862731X-RAY DIFFRACTION100
2.7692-2.82250.39281430.35262621X-RAY DIFFRACTION100
2.8225-2.88010.35931350.33742670X-RAY DIFFRACTION100
2.8801-2.94270.38041430.33012754X-RAY DIFFRACTION100
2.9427-3.01110.33241390.30682599X-RAY DIFFRACTION100
3.0111-3.08640.32611460.29852772X-RAY DIFFRACTION100
3.0864-3.16990.3121360.30032602X-RAY DIFFRACTION100
3.1699-3.26310.34261480.29052717X-RAY DIFFRACTION100
3.2631-3.36840.36551340.29042625X-RAY DIFFRACTION100
3.3684-3.48880.31911470.26992678X-RAY DIFFRACTION99
3.4888-3.62840.35071440.24822714X-RAY DIFFRACTION100
3.6284-3.79350.29571440.25682613X-RAY DIFFRACTION100
3.7935-3.99350.31471380.2472660X-RAY DIFFRACTION99
3.9935-4.24350.29311420.23292669X-RAY DIFFRACTION99
4.2435-4.5710.25981330.22182677X-RAY DIFFRACTION99
4.571-5.03060.30741330.20322669X-RAY DIFFRACTION99
5.0306-5.75770.27511440.23462673X-RAY DIFFRACTION100
5.7577-7.25060.29381360.23832686X-RAY DIFFRACTION100
7.2506-50.55020.2861390.22642579X-RAY DIFFRACTION97
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)
12.74760.6833-0.90661.15830.43483.03280.1057-0.00150.27330.13840.07270.1439-0.0898-0.3573-0.16810.35210.1052-0.0020.34740.06690.3009-20.3273-10.913266.6786
25.0937-1.54661.8152.9702-1.77648.3899-0.106-0.1447-0.6071-0.2160.2254-0.07530.43410.2694-0.13350.31350.05550.04230.2151-0.07950.3128-11.7479-16.104349.8806
32.6065-0.2778-0.11412.78710.93890.6544-0.23050.22690.7044-0.49010.07890.4208-0.1655-0.02010.11560.4098-0.1193-0.09690.46090.01310.5627-33.40829.025621.8639
41.38520.8282-1.86860.7308-1.29612.60640.6303-0.51290.330.63290.13190.4401-0.4660.2819-0.38151.0243-0.3099-0.63660.64490.02551.2511-24.049932.44128.4768
53.23050.6252-0.08743.18490.68320.5405-0.1817-0.21470.5229-0.11630.07990.0489-0.05240.09370.11090.3114-0.0211-0.03770.4669-0.01410.2971-28.4698.942930.6669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:265)
2X-RAY DIFFRACTION2(chain A and resid 266:326)
3X-RAY DIFFRACTION3(chain A and resid 327:612)
4X-RAY DIFFRACTION4(chain A and resid 613:658)
5X-RAY DIFFRACTION5(chain A and resid 659:865)

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