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- PDB-9imr: Crystal structure of geranylgeranyl pyrophosphate synthase Rv0562... -

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Basic information

Entry
Database: PDB / ID: 9imr
TitleCrystal structure of geranylgeranyl pyrophosphate synthase Rv0562 from Mycobacterium tuberculosis in complex with IPP
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 / prenyltransferase activity / (2E,6E)-farnesyl diphosphate synthase / 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 / prenyltransferase activity / (2E,6E)-farnesyl diphosphate synthase / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Nonaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 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

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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)73,08617
Polymers71,1972
Non-polymers1,88915
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-87 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.796, 115.643, 119.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 934 molecules

#2: Chemical
ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 30% PEG 6000, 0.6 M Bicine, pH 9.0

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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: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.89→35.96 Å / Num. obs: 54521 / % possible obs: 99.1 % / Redundancy: 7.04 % / Rmerge(I) obs: 0.0402 / Net I/σ(I): 30.7
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.1302 / Mean I/σ(I) obs: 6.75 / Num. unique obs: 2344 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→32.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.551 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2697 5 %RANDOM
Rwork0.14156 ---
obs0.14419 51618 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.037 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.57 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.89→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 113 919 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174868
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.6436916
X-RAY DIFFRACTIONr_angle_other_deg1.4921.57511194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3335662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3920.803274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58715809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.841553
X-RAY DIFFRACTIONr_chiral_restr0.0880.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021062
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_it1.411.4392651
X-RAY DIFFRACTIONr_mcbond_other1.411.4392649
X-RAY DIFFRACTIONr_mcangle_it2.0642.153309
X-RAY DIFFRACTIONr_mcangle_other2.0642.153309
X-RAY DIFFRACTIONr_scbond_it2.5531.7582448
X-RAY DIFFRACTIONr_scbond_other2.5531.7582449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9672.5253607
X-RAY DIFFRACTIONr_long_range_B_refined5.75419.9146365
X-RAY DIFFRACTIONr_long_range_B_other5.75419.9166366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 181 -
Rwork0.176 3583 -
obs--94.5 %

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