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- PDB-5h9d: Crystal structure of Heptaprenyl Diphosphate Synthase from Staphy... -

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Basic information

Entry
Database: PDB / ID: 5h9d
TitleCrystal structure of Heptaprenyl Diphosphate Synthase from Staphylococcus aureus
Components
  • C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
  • Farnesyl pyrophosphate synthetase
  • Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
KeywordsTRANSFERASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase
Function / homology
Function and homology information


heptaprenyl diphosphate synthase activity / heptaprenyl diphosphate synthase / dimethylallyltranstransferase / prenyltransferase activity / menaquinone biosynthetic process / isoprenoid biosynthetic process / dimethylallyltranstransferase activity
Similarity search - Function
Heptaprenyl diphosphate synthase subunit 1 / Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 / Hexaprenyl diphosphate synthase, small subunit / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Heptaprenyl diphosphate synthase subunit 1 / Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 / Hexaprenyl diphosphate synthase, small subunit / 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
PHOSPHATE ION / Farnesyl pyrophosphate synthetase / Heptaprenyl pyrophosphate synthase subunit A / Heptaprenyl diphosphate syntase component II, putative / Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsWei, H.L. / Liu, W.D. / Zheng, Y.Y. / Ko, T.P. / Chen, C.C. / Guo, R.T.
CitationJournal: ChemMedChem / Year: 2016
Title: Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase
Authors: Desai, J. / Liu, Y.L. / Wei, H. / Liu, W. / Ko, T.P. / Guo, R.T. / Oldfield, E.
History
DepositionDec 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Mar 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: Farnesyl pyrophosphate synthetase
B: Farnesyl pyrophosphate synthetase
C: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
D: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
K: C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
L: C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,33810
Polymers120,9596
Non-polymers3804
Water2,126118
1
A: Farnesyl pyrophosphate synthetase
C: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
K: C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7646
Polymers60,4793
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Farnesyl pyrophosphate synthetase
D: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
L: C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5744
Polymers60,4793
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.394, 137.642, 144.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21D-218-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthetase / Heptaprenyl diphosphate syntase component II / Heptaprenyl diphosphate synthase


Mass: 36199.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: hepT, gerCC, AFO87_08490, AL078_00755, AL493_08930, AL498_03950, AL508_07350, AM595_07380, CH51_07695, EQ80_006970, ER12_006960, ERS092844_00891, ERS093009_01199, ERS195423_01812, ERS365775_ ...Gene: hepT, gerCC, AFO87_08490, AL078_00755, AL493_08930, AL498_03950, AL508_07350, AM595_07380, CH51_07695, EQ80_006970, ER12_006960, ERS092844_00891, ERS093009_01199, ERS195423_01812, ERS365775_02304, ERS410449_02217, ERS411009_00914, ERS411017_01500, ERS445052_01888, FE68_02720, RL02_11030, RT87_07355, SAMI_1402
Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D6HKK2, UniProt: Q2FYG6*PLUS, dimethylallyltranstransferase, heptaprenyl diphosphate synthase
#2: Protein Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein / Heptaprenyl pyrophosphate synthase subunit A


Mass: 22185.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: AL078_00765, AM595_07390, AUC48_07185, AUC49_07360, AUC50_07510, BN1321_260110, ERS179246_00728, ERS445051_01360, NI36_07270, RT87_07365, SA7112_09025, SAFDA_1366, SAMI_1404, SASCBU26_01375
Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8TTD5
#3: Protein/peptide C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family protein


Mass: 2093.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8TTD5, UniProt: Q2FYG4*PLUS
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Citic acid, bis-tris propane, PEG 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: Apr 9, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→25 Å / Num. obs: 35313 / % possible obs: 92 % / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 2.258 / Net I/av σ(I): 38.038 / Net I/σ(I): 25 / Num. measured all: 175144
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.7850.4835820.8780.2290.5341.66294.3
2.78-2.8950.35235450.930.1670.3921.71393.9
2.89-3.0250.24835550.9690.1180.2761.8293.8
3.02-3.1850.16335550.9830.0770.1811.94693.5
3.18-3.385.10.11135540.9910.0520.1232.05993.1
3.38-3.6450.07635140.9950.0360.0842.4892.2
3.64-44.90.05635370.9970.0270.0632.94492.1
4-4.584.90.04135230.9980.0190.0462.92591.4
4.58-5.754.90.03535250.9990.0160.0392.69290.6
5.751-254.70.02734230.9990.0130.0312.4285.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
CNS1.21refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: Chains K/L are built from residual densities exist between the neighboring heterodimers. Author persume Chains K/L come from a neighboring heterodimer with the region 140-170 of the protein unfolded.
RfactorNum. reflection% reflection
Rfree0.2867 1662 4.3 %
Rwork0.2435 31869 -
obs-33531 86.9 %
Solvent computationBsol: 50.3455 Å2
Displacement parametersBiso max: 148.41 Å2 / Biso mean: 75.7839 Å2 / Biso min: 37.28 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å2-0 Å20 Å2
2--8.039 Å20 Å2
3----13.759 Å2
Refinement stepCycle: LAST / Resolution: 2.68→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8446 0 20 130 8596
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3471.5
X-RAY DIFFRACTIONc_scbond_it1.8122
X-RAY DIFFRACTIONc_mcangle_it2.3272
X-RAY DIFFRACTIONc_scangle_it2.7872.5

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