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- PDB-9k9c: Crystal structure of Sorghum bicolor SPS complexed with Zoledronate -

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Basic information

Entry
Database: PDB / ID: 9k9c
TitleCrystal structure of Sorghum bicolor SPS complexed with Zoledronate
ComponentsSolanesyl diphosphate synthase
KeywordsTRANSFERASE / inhibitor / chloroplast
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / plastoquinone biosynthetic process / isoprenoid biosynthetic process / chloroplast / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
ZOLEDRONIC ACID / all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.286 Å
AuthorsXiao, H. / Li, M. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of Sorghum bicolor SPS complexed with Zoledronate
Authors: Xiao, H. / Li, M. / Yang, G.-F.
History
DepositionOct 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,8256
Polymers70,4802
Non-polymers3454
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-57 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.228, 55.972, 93.358
Angle α, β, γ (deg.)90.00, 106.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Solanesyl diphosphate synthase


Mass: 35239.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: BDA96_09G261500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A921QCV5
#2: Chemical ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID


Mass: 272.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Potassium thiocyanate, Bis-Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.286→46.37 Å / Num. obs: 30378 / % possible obs: 99.41 % / Redundancy: 10.204 % / CC1/2: 0.995 / Net I/σ(I): 7.95
Reflection shellResolution: 2.286→2.368 Å / Num. unique obs: 2977 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.286→46.368 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 1518 5 %
Rwork0.2097 --
obs0.2118 30339 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.286→46.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 19 117 4788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024722
X-RAY DIFFRACTIONf_angle_d0.4556389
X-RAY DIFFRACTIONf_dihedral_angle_d5.2322864
X-RAY DIFFRACTIONf_chiral_restr0.034755
X-RAY DIFFRACTIONf_plane_restr0.003828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2863-2.36010.27371350.23762565X-RAY DIFFRACTION99
2.3601-2.44440.27171370.22242610X-RAY DIFFRACTION99
2.4444-2.54230.25841370.23252605X-RAY DIFFRACTION100
2.5423-2.6580.28461380.22682608X-RAY DIFFRACTION100
2.658-2.79810.28151370.21872607X-RAY DIFFRACTION100
2.7981-2.97340.25951380.22352611X-RAY DIFFRACTION100
2.9734-3.20290.28371370.22062622X-RAY DIFFRACTION100
3.2029-3.52510.2821390.22352636X-RAY DIFFRACTION100
3.5251-4.0350.20081390.19482630X-RAY DIFFRACTION99
4.035-5.08260.23761380.18642626X-RAY DIFFRACTION99
5.0826-100.2391430.20552701X-RAY DIFFRACTION99

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