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- PDB-5zlf: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHE... -

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Basic information

Entry
Database: PDB / ID: 5zlf
TitleCRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH ligand BPH-629
ComponentsOctaprenyl diphosphate synthase
KeywordsTRANSFERASE/INHIBITOR / PRENYLTRANSFERASE / SITE-DIRECTED MUTAGENESIS / PRODUCT CHAIN LENGTH / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


all-trans-octaprenyl-diphosphate synthase / octaprenyl pyrophosphate synthase activity / polyprenol biosynthetic process / prenyltransferase activity / ubiquinone biosynthetic process / isoprenoid biosynthetic process / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B29 / Octaprenyl diphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.845 Å
AuthorsHan, X. / 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 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 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: Octaprenyl diphosphate synthase
B: Octaprenyl diphosphate synthase
C: Octaprenyl diphosphate synthase
D: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4967
Polymers141,0004
Non-polymers4973
Water1086
1
A: Octaprenyl diphosphate synthase
B: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9724
Polymers70,5002
Non-polymers4732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-47 kcal/mol
Surface area25510 Å2
MethodPISA
2
C: Octaprenyl diphosphate synthase
D: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5243
Polymers70,5002
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-37 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.344, 46.645, 215.741
Angle α, β, γ (deg.)90.000, 101.080, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 86 or resid 103...
21(chain B and (resid 2 through 153 or resid 164 through 320))
31(chain C and (resid 2 through 86 or resid 103...
41(chain D and (resid 2 through 86 or resid 103...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 86 or resid 103...A2 - 86
121(chain A and (resid 2 through 86 or resid 103...A103 - 153
131(chain A and (resid 2 through 86 or resid 103...A164 - 214
141(chain A and (resid 2 through 86 or resid 103...A231 - 241
151(chain A and (resid 2 through 86 or resid 103...A265 - 278
161(chain A and (resid 2 through 86 or resid 103...A282 - 320
211(chain B and (resid 2 through 153 or resid 164 through 320))B2 - 153
221(chain B and (resid 2 through 153 or resid 164 through 320))B164 - 320
311(chain C and (resid 2 through 86 or resid 103...C2 - 86
321(chain C and (resid 2 through 86 or resid 103...C103 - 153
331(chain C and (resid 2 through 86 or resid 103...C164 - 214
341(chain C and (resid 2 through 86 or resid 103...C231 - 241
351(chain C and (resid 2 through 86 or resid 103...C265 - 278
361(chain C and (resid 2 through 86 or resid 103...C282 - 320
411(chain D and (resid 2 through 86 or resid 103...D2 - 86
421(chain D and (resid 2 through 86 or resid 103...D103 - 153
431(chain D and (resid 2 through 86 or resid 103...D2 - 320
441(chain D and (resid 2 through 86 or resid 103...D231 - 241
451(chain D and (resid 2 through 86 or resid 103...D265 - 320

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Components

#1: Protein
Octaprenyl diphosphate synthase / All-trans-octaprenyl-diphosphate synthase / Octaprenyl pyrophosphate synthase / OPP synthase


Mass: 35249.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ispB, cel, yhbD, b3187, JW3154 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB(DE3)
References: UniProt: P0AD57, all-trans-octaprenyl-diphosphate synthase
#2: Chemical ChemComp-B29 / [2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID / [2-(3-DIBENZO[B,D]FURAN-4-YLPHENYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)


Mass: 448.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18O8P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.62 Å3/Da / Density % sol: 52.96 % / Mosaicity: 0.574 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS-HCL, 24%(W/V) POLYETHYLENE GLYCOL 3350

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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: Aug 26, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. obs: 34599 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.082 / Χ2: 0.967 / Net I/σ(I): 11.6 / Num. measured all: 150953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.954.40.58234270.8020.3190.6661.087100
2.95-3.074.40.40734200.8840.2230.4651.018100
3.07-3.214.40.31534280.9220.1710.361.029100
3.21-3.384.40.23734460.9580.1280.271.07100
3.38-3.594.40.15334340.9810.0820.1740.988100
3.59-3.874.40.09934430.9920.0530.1130.871100
3.87-4.254.40.06734540.9960.0350.0750.82100
4.25-4.864.40.07234620.9940.0370.0821.13699.9
4.86-6.114.30.05634770.9980.0290.0630.861100
6.11-254.10.03736080.9980.0210.0430.78499.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJK

3wjk


Resolution: 2.845→24.871 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.04
RfactorNum. reflection% reflection
Rfree0.2986 1730 5 %
Rwork0.2407 --
obs0.2435 34589 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 355.73 Å2 / Biso mean: 103.517 Å2 / Biso min: 28.99 Å2
Refinement stepCycle: final / Resolution: 2.845→24.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8626 0 32 6 8664
Biso mean--120.28 53.92 -
Num. residues----1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098974
X-RAY DIFFRACTIONf_angle_d1.59212164
X-RAY DIFFRACTIONf_chiral_restr0.1221425
X-RAY DIFFRACTIONf_plane_restr0.0081586
X-RAY DIFFRACTIONf_dihedral_angle_d14.2035407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4446X-RAY DIFFRACTION20.385TORSIONAL
12B4446X-RAY DIFFRACTION20.385TORSIONAL
13C4446X-RAY DIFFRACTION20.385TORSIONAL
14D4446X-RAY DIFFRACTION20.385TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8446-2.92820.36661250.32452375250086
2.9282-3.02260.31431430.307227182861100
3.0226-3.13040.33981460.285127802926100
3.1304-3.25550.38291430.292727162859100
3.2555-3.40330.36641460.288627702916100
3.4033-3.58220.33581440.262127342878100
3.5822-3.80590.25761440.237427382882100
3.8059-4.09860.2971460.23227722918100
4.0986-4.50890.27121460.206227652911100
4.5089-5.15620.2641480.217728092957100
5.1562-6.47730.31771470.25727972944100
6.4773-24.87240.28281520.21922885303799
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)
11.77070.2158-0.50990.5179-0.04342.90940.0660.55530.2788-0.1549-0.0616-0.1933-0.4188-0.8989-0.06730.83090.05760.0040.80290.06580.428156.71762.227128.1313
21.2612-0.0512-0.85171.84630.30741.7243-0.0921-0.1362-0.13290.559-0.0874-0.3830.49060.19550.00050.5824-0.0303-0.02010.48880.13420.613487.3467-13.105230.3392
32.70.7086-0.08442.6123-0.80163.50630.0877-0.22960.06530.0641-0.1766-0.2796-0.27590.52920.00130.3521-0.0773-0.01690.3571-0.01380.426868.44044.18278.264
43.2912-0.4777-0.44672.19340.44633.0738-0.17980.0617-0.3227-0.0224-0.00110.02581.1596-1.1838-0.27690.555-0.4402-0.00710.7276-0.01550.436536.5519-10.362577.1352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 319)A2 - 319
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 320)B1 - 320
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 320)C1 - 320
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 320)D2 - 320

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