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- PDB-9ims: Crystal structure of C45 isoprenyl diphosphate synthase Rv0562 va... -

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Basic information

Entry
Database: PDB / ID: 9ims
TitleCrystal structure of C45 isoprenyl diphosphate synthase Rv0562 variant D98R/D223R 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: 2.27 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)71,6033
Polymers71,3652
Non-polymers2381
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-30 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.738, 108.815, 56.062
Angle α, β, γ (deg.)90.00, 95.41, 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: 35682.461 Da / Num. of mol.: 2 / Mutation: D98R, D223R
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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 12% PEG 6000, 0.1 M MES, pH 6.0, 2 M LiCl

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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: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.27→35.96 Å / Num. obs: 30511 / % possible obs: 99 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.0747 / Net I/σ(I): 10.72
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.3301 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 1508 / % possible all: 95.6

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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: 2.27→27.27 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 1511 5.04 %RANDOM
Rwork0.197 ---
obs0.2008 29983 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 16 351 4623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.881
X-RAY DIFFRACTIONf_dihedral_angle_d5.463630
X-RAY DIFFRACTIONf_chiral_restr0.046704
X-RAY DIFFRACTIONf_plane_restr0.008759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.340.27661020.2132403X-RAY DIFFRACTION90
2.34-2.430.27381170.20472496X-RAY DIFFRACTION94
2.43-2.520.30371390.21012513X-RAY DIFFRACTION95
2.52-2.640.29611290.21612559X-RAY DIFFRACTION97
2.64-2.780.28981620.212603X-RAY DIFFRACTION99
2.78-2.950.34671200.22062662X-RAY DIFFRACTION100
2.95-3.180.30821400.21082616X-RAY DIFFRACTION100
3.18-3.50.26471360.20832666X-RAY DIFFRACTION99
3.5-40.24121370.16752654X-RAY DIFFRACTION100
4-5.040.23091500.17122643X-RAY DIFFRACTION100
5.04-27.270.26381790.20362657X-RAY DIFFRACTION100

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