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- PDB-9imq: Crystal structure of a C45 isoprenyl diphosphate synthase, Rv0562... -

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Basic information

Entry
Database: PDB / ID: 9imq
TitleCrystal structure of a C45 isoprenyl diphosphate synthase, Rv0562 from Mycobacterium tuberculosis
ComponentsNonaprenyl diphosphate synthase
KeywordsTRANSFERASE / geranylgeranyl pyrophosphate synthase / isoprenyl diphosphate synthases / terpenoids
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / isoprenoid biosynthetic process / (2E,6E)-farnesyl diphosphate synthase activity / peptidoglycan-based cell wall ...all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / isoprenoid biosynthetic process / (2E,6E)-farnesyl diphosphate synthase activity / peptidoglycan-based cell wall / metal ion binding / plasma membrane
Similarity search - Function
: / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Nonaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWang, Q. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural insight of a bi-functional isoprenyl diphosphate synthase Rv0562 from Mycobacterium tuberculosis.
Authors: Wang, Q. / Yang, Y. / He, B. / Huang, J.W. / Kuo, C.J. / Chen, C.C. / Guo, R.T.
History
DepositionJul 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nonaprenyl diphosphate synthase
B: Nonaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2695
Polymers71,1972
Non-polymers733
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-50 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.882, 90.376, 59.032
Angle α, β, γ (deg.)90.00, 101.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nonaprenyl diphosphate synthase / (2E / 6E)-farnesyl diphosphate synthase / E / E-FPP synthase / FPP synthase / Geranylgeranyl ...(2E / 6E)-farnesyl diphosphate synthase / E / E-FPP synthase / FPP synthase / Geranylgeranyl diphosphate synthase / GGPP synthase / GGPS


Mass: 35598.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: grcC1, Rv0562 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06428, all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific], (2E,6E)-farnesyl diphosphate synthase, geranylgeranyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES 7.5 2% PEG 400 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.54→35.96 Å / Num. obs: 18703 / % possible obs: 99.6 % / Redundancy: 3.33 % / Rmerge(I) obs: 0.0783 / Net I/σ(I): 9.11
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 3.05 % / Rmerge(I) obs: 0.3271 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 873 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→26.92 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 933 5.05 %RANDOM
Rwork0.1877 ---
obs0.1921 18475 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 3 187 4872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.879
X-RAY DIFFRACTIONf_dihedral_angle_d5.762681
X-RAY DIFFRACTIONf_chiral_restr0.048765
X-RAY DIFFRACTIONf_plane_restr0.008849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.670.33031240.2282453X-RAY DIFFRACTION97
2.67-2.840.32071420.22352496X-RAY DIFFRACTION99
2.84-3.060.32261600.21812476X-RAY DIFFRACTION99
3.06-3.370.31371230.21162523X-RAY DIFFRACTION99
3.37-3.850.26681270.17132522X-RAY DIFFRACTION99
3.85-4.850.21971420.14832496X-RAY DIFFRACTION99
4.85-4.860.27051150.19192576X-RAY DIFFRACTION99

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