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- PDB-5ze6: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHE... -

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Basic information

Entry
Database: PDB / ID: 5ze6
TitleCRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981
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 activity / all-trans-octaprenyl-diphosphate synthase / polyprenol biosynthetic process / prenyltransferase activity / ubiquinone biosynthetic process / isoprenoid biosynthetic process / protein homodimerization activity / metal ion binding / identical protein 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
2-hydroxy-6-(tetradecyloxy)benzoic acid / Octaprenyl diphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionFeb 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 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

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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)141,7498
Polymers141,0004
Non-polymers7504
Water7,512417
1
A: Octaprenyl diphosphate synthase
C: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8503
Polymers70,5002
Non-polymers3501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-33 kcal/mol
Surface area25300 Å2
MethodPISA
2
B: Octaprenyl diphosphate synthase
D: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8995
Polymers70,5002
Non-polymers3993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-52 kcal/mol
Surface area24760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.032, 111.999, 133.822
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
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AD57, all-trans-octaprenyl-diphosphate synthase
#2: Chemical ChemComp-HJX / 2-hydroxy-6-(tetradecyloxy)benzoic acid / BPH-981


Mass: 350.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34O4
#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.: 417 / 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: 2.61 Å3/Da / Density % sol: 52.8 % / Mosaicity: 0.51 °
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 315r / 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: 2.5→25 Å / Num. obs: 49730 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.451 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.595.90.49549021.4381100
2.59-2.695.90.41449061.4921100
2.69-2.825.90.35349091.5421100
2.82-2.965.90.26949301.6121100
2.96-3.155.90.20549261.6551100
3.15-3.395.90.1449291.4541100
3.39-3.735.90.08749801.3581100
3.73-4.275.70.06849761.4511100
4.27-5.375.80.05150401.321100
5.37-255.60.03252321.188199.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJK

3wjk


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.964 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26405 2427 4.9 %RANDOM
Rwork0.18544 ---
obs0.18931 47239 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--1.3 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9411 0 52 417 9880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199608
X-RAY DIFFRACTIONr_bond_other_d0.0010.028980
X-RAY DIFFRACTIONr_angle_refined_deg1.491.96713016
X-RAY DIFFRACTIONr_angle_other_deg0.91320790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75651222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36725.299451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.361151629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3831556
X-RAY DIFFRACTIONr_chiral_restr0.0920.21506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210804
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021792
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_it3.7083.9654921
X-RAY DIFFRACTIONr_mcbond_other3.7073.9644920
X-RAY DIFFRACTIONr_mcangle_it5.4645.9266132
X-RAY DIFFRACTIONr_mcangle_other5.4645.9276133
X-RAY DIFFRACTIONr_scbond_it4.4384.4514687
X-RAY DIFFRACTIONr_scbond_other4.4364.4464684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6116.496885
X-RAY DIFFRACTIONr_long_range_B_refined9.5937541442
X-RAY DIFFRACTIONr_long_range_B_other9.59674.99841294
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 178 -
Rwork0.228 3338 -
obs--97.29 %

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