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- PDB-5zhe: STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 5zhe
TitleSTRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-981
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
KeywordsTRANSFERASE/INHIBITOR / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / 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 / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium 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 / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / protein homodimerization activity / 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
2-hydroxy-6-(tetradecyloxy)benzoic acid / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGao, J. / Liu, W.D. / Zheng, Y.Y. / Ko, T.P. / Chen, C.C. / Guo, R.T.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.
Authors: Malwal, S.R. / Chen, L. / Hicks, H. / Qu, F. / Liu, W. / Shillo, A. / Law, W.X. / Zhang, J. / Chandnani, N. / Han, X. / Zheng, Y. / Chen, C.C. / Guo, R.T. / AbdelKhalek, A. / Seleem, M.N. / Oldfield, E.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
B: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3133
Polymers56,9622
Non-polymers3501
Water2,342130
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-15 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.713, 68.449, 109.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) / Ditrans / polycis-undecaprenylcistransferase


Mass: 28481.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ispU, rth, uppS, yaeS, b0174, JW0169 / Plasmid: pET32EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-HJX / 2-hydroxy-6-(tetradecyloxy)benzoic acid / BPH-981


Mass: 350.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.09 Å3/Da / Density % sol: 41.18 % / Mosaicity: 0.41 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 % ETHYLENE GLYCOL, 2-5% PEG 35K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→25 Å / Num. obs: 25466 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.044 / Χ2: 0.827 / Net I/σ(I): 18.4 / Num. measured all: 160471
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.18-2.2650.2624350.548197.6
2.26-2.3560.24125090.557199.8
2.35-2.456.60.16625300.5741100
2.45-2.586.70.12825150.6111100
2.58-2.756.70.08825510.697199.9
2.75-2.966.70.06125120.815199.9
2.96-3.256.60.04425610.9731100
3.25-3.726.50.03725821.11100
3.72-4.696.30.04125960.9921100
4.69-2560.0326751.317197.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WYJ

3wyj


Resolution: 2.18→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.147 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26308 1166 4.6 %RANDOM
Rwork0.20309 ---
obs0.20586 24247 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.869 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å20 Å2
2--1.3 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.18→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 25 130 3378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193328
X-RAY DIFFRACTIONr_bond_other_d0.0010.023069
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9254483
X-RAY DIFFRACTIONr_angle_other_deg0.92537062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5323.39177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3615558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8921533
X-RAY DIFFRACTIONr_chiral_restr0.1050.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0474.8791627
X-RAY DIFFRACTIONr_mcbond_other6.0484.8781626
X-RAY DIFFRACTIONr_mcangle_it7.8937.2722025
X-RAY DIFFRACTIONr_mcangle_other7.8917.2732026
X-RAY DIFFRACTIONr_scbond_it7.4215.7851701
X-RAY DIFFRACTIONr_scbond_other7.3935.7741698
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.5068.3352459
X-RAY DIFFRACTIONr_long_range_B_refined13.5692.88213717
X-RAY DIFFRACTIONr_long_range_B_other13.55992.85713673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 86 -
Rwork0.237 1660 -
obs--96.15 %

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