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- PDB-3th8: Structure of E. coli undecaprenyl diphosphate synthase complexed ... -

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Basic information

Entry
Database: PDB / ID: 3th8
TitleStructure of E. coli undecaprenyl diphosphate synthase complexed with BPH-1063
ComponentsUndecaprenyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / all helices / prenyl transferase / farneyl diphosphate binding / Isopentenyl diphosphate binding / prenylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding / regulation of cell shape / cell cycle / cell division / magnesium ion binding / protein homodimerization activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TH9 / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.114 Å
AuthorsCao, R. / Zhu, W. / Zhang, Y. / Oldfield, E.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis.
Authors: Zhang, Y. / Lin, F.-Y. / Li, K. / Zhu, W. / Liu, Y.L. / Cao, R. / Pang, R. / Lee, E. / Axelson, J. / Hensler, M. / Wang, K. / Molohon, K.J. / Wang, Y. / Mitchell, D.A. / Nizet, V. / Oldfield, E.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Undecaprenyl pyrophosphate synthase
A: Undecaprenyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3123
Polymers56,9622
Non-polymers3491
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-12 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.603, 68.862, 112.297
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 Undecaprenyl pyrophosphate synthase / UPP synthase / Di-trans / poly-cis-decaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS


Mass: 28481.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uppS, ispU, rth, yaeS, b0174, JW0169 / Production host: Escherichia coli (E. coli)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-TH9 / (2Z)-4-({3-[3-(hexyloxy)phenyl]propyl}amino)-2-hydroxy-4-oxobut-2-enoic acid / BPH-1063


Mass: 349.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.114→50 Å / Num. obs: 27971 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.114→2.16 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E98

2e98


Resolution: 2.114→41.8 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.312 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 1400 5.1 %RANDOM
Rwork0.2495 ---
all0.2525 29046 --
obs0.2525 27646 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.71 Å2 / Biso mean: 35.9978 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.114→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 25 63 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213402
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9244586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1225412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79723.37181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31415572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4811534
X-RAY DIFFRACTIONr_chiral_restr0.1250.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022627
X-RAY DIFFRACTIONr_mcbond_it1.1861.52049
X-RAY DIFFRACTIONr_mcangle_it2.10423255
X-RAY DIFFRACTIONr_scbond_it3.23631353
X-RAY DIFFRACTIONr_scangle_it5.154.51331
LS refinement shellResolution: 2.114→2.169 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 101 -
Rwork0.369 1779 -
all-1880 -
obs--91.26 %

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