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- PDB-5hv2: Rifampin phosphotransferase G527Y mutant from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 5hv2
TitleRifampin phosphotransferase G527Y mutant from Listeria monocytogenes
ComponentsPhosphoenolpyruvate synthase
KeywordsTRANSFERASE / Antibiotic resistance / Rifampin / Phosphotransferase
Function / homology
Function and homology information


Phosphohistidine domain / Glucose Oxidase; domain 1 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.912 Å
AuthorsZhang, P. / Qi, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis of rifampin inactivation by rifampin phosphotransferase
Authors: Qi, X. / Lin, W. / Ma, M. / Wang, C. / He, Y. / He, N. / Gao, J. / Zhou, H. / Xiao, Y. / Wang, Y. / Zhang, P.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate synthase


Theoretical massNumber of molelcules
Total (without water)98,5031
Polymers98,5031
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area40320 Å2
Unit cell
Length a, b, c (Å)58.751, 128.760, 142.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Phosphoenolpyruvate synthase / rifampin phosphotransferase


Mass: 98503.312 Da / Num. of mol.: 1 / Fragment: UNP residues 1-867 / Mutation: G527Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: ATE46_07415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2YLC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.4
Details: 19%(w/v) PEG8000, 100 mM Tris-HCl, 200 mM lithium chloride

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 24022 / % possible obs: 99.1 % / Redundancy: 4.1 % / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.912→43.397 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2010 8.48 %
Rwork0.2119 --
obs0.2168 23700 91.778 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.912→43.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 0 1 6611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116730
X-RAY DIFFRACTIONf_angle_d1.5039103
X-RAY DIFFRACTIONf_dihedral_angle_d19.7392525
X-RAY DIFFRACTIONf_chiral_restr0.061040
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.912-2.98480.3161960.30711033X-RAY DIFFRACTION35
2.9848-3.06550.41951400.28841501X-RAY DIFFRACTION50
3.0655-3.15570.3411410.27791528X-RAY DIFFRACTION52
3.1557-3.25750.32911450.27321566X-RAY DIFFRACTION52
3.2575-3.37390.35561450.26011552X-RAY DIFFRACTION52
3.3739-3.50890.30291450.25951562X-RAY DIFFRACTION52
3.5089-3.66850.29481470.22791585X-RAY DIFFRACTION53
3.6685-3.86180.27381450.21561564X-RAY DIFFRACTION53
3.8618-4.10360.26891460.19981567X-RAY DIFFRACTION53
4.1036-4.42020.22971480.19081593X-RAY DIFFRACTION53
4.4202-4.86440.21251480.1731598X-RAY DIFFRACTION54
4.8644-5.56710.24581490.19141599X-RAY DIFFRACTION54
5.5671-7.00920.30231560.20451676X-RAY DIFFRACTION56
7.0092-43.40190.19321590.16761766X-RAY DIFFRACTION59

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