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- PDB-5hv1: Rifampin phosphotransferase in complex with AMPPNP and rifampin f... -

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Basic information

Entry
Database: PDB / ID: 5hv1
TitleRifampin phosphotransferase in complex with AMPPNP and rifampin from Listeria monocytogenes
ComponentsPhosphoenolpyruvate synthase
KeywordsTRANSFERASE / Antibiotic resistance / Rifampin / Phosphotransferase
Function / homologyATP-grasp fold, A domain / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RIFAMPICIN / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.103 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1674
Polymers98,8141
Non-polymers1,3533
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.090, 151.090, 191.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Phosphoenolpyruvate synthase / rifampin phosphotransferase


Mass: 98813.680 Da / Num. of mol.: 1 / Fragment: UNP residues 1-867
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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 9.2 / Details: 18%(w/v) PEG3350, 100 mM Bicine

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.1→30.019 Å / Num. obs: 23960 / % possible obs: 99.7 % / Redundancy: 26.6 % / Net I/σ(I): 28.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 3.103→30.019 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2863 1835 8.72 %
Rwork0.2497 --
obs0.253 21038 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.103→30.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6663 0 91 3 6757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186878
X-RAY DIFFRACTIONf_angle_d2.1299320
X-RAY DIFFRACTIONf_dihedral_angle_d19.9292585
X-RAY DIFFRACTIONf_chiral_restr0.3421065
X-RAY DIFFRACTIONf_plane_restr0.0071188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1026-3.14330.3713810.3812850X-RAY DIFFRACTION54
3.1433-3.18640.3633930.3354985X-RAY DIFFRACTION64
3.1864-3.23180.45991080.34651125X-RAY DIFFRACTION73
3.2318-3.280.34461300.3281391X-RAY DIFFRACTION88
3.28-3.33120.4361400.32451491X-RAY DIFFRACTION97
3.3312-3.38570.35471430.30251544X-RAY DIFFRACTION99
3.3857-3.4440.31311510.29151559X-RAY DIFFRACTION100
3.444-3.50660.36631460.30561545X-RAY DIFFRACTION100
3.5066-3.57390.31361480.28181545X-RAY DIFFRACTION100
3.5739-3.64670.32861490.27241575X-RAY DIFFRACTION100
3.6467-3.72590.31091420.27771537X-RAY DIFFRACTION100
3.7259-3.81240.27261470.27521550X-RAY DIFFRACTION100
3.8124-3.90750.28311450.25181543X-RAY DIFFRACTION100
3.9075-4.0130.31321470.24471566X-RAY DIFFRACTION100
4.013-4.13080.26411490.24281536X-RAY DIFFRACTION100
4.1308-4.26370.2861520.23261564X-RAY DIFFRACTION100
4.2637-4.41570.25581550.21481531X-RAY DIFFRACTION100
4.4157-4.59190.20621490.21161569X-RAY DIFFRACTION100
4.5919-4.80.22141470.21221536X-RAY DIFFRACTION100
4.8-5.0520.2671490.22791567X-RAY DIFFRACTION100
5.052-5.36680.27091540.24321532X-RAY DIFFRACTION100
5.3668-5.77850.29811470.24531567X-RAY DIFFRACTION100
5.7785-6.3550.26921450.26691557X-RAY DIFFRACTION100
6.355-7.26320.29531470.23581552X-RAY DIFFRACTION100
7.2632-9.10830.27411550.22851549X-RAY DIFFRACTION100
9.1083-30.01990.23551500.19081541X-RAY DIFFRACTION99

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