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- PDB-9jzf: Crystal structure of OsSPS3 complexed with zoledronate and isopen... -

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Basic information

Entry
Database: PDB / ID: 9jzf
TitleCrystal structure of OsSPS3 complexed with zoledronate and isopentenyl diphosphate
ComponentsProbable solanesyl-diphosphate synthase 3, chloroplastic
KeywordsTRANSFERASE / inhibitor / chloroplast
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific] / plastoquinone biosynthetic process / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / prenyltransferase activity / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ZOLEDRONIC ACID / Probable solanesyl-diphosphate synthase 3, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 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 OsSPS3 complexed with zoledronate and isopentenyl diphosphate
Authors: Xiao, H. / Li, M. / Yang, G.-F.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable solanesyl-diphosphate synthase 3, chloroplastic
B: Probable solanesyl-diphosphate synthase 3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7727
Polymers71,1812
Non-polymers5915
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-50 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.048, 90.718, 125.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable solanesyl-diphosphate synthase 3, chloroplastic / OsSPS3 / Probable all-trans-nonaprenyl-diphosphate synthase 3 (geranyl-diphosphate specific)


Mass: 35590.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: SPS3, Os12g0271700, LOC_Os12g17320, OsJ_1767i3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0INZ4, all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific]
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / Comment: medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Tris, Ammonium sulfate

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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: 2.446→48.293 Å / Num. obs: 24483 / % possible obs: 98.73 % / Redundancy: 10.244 % / CC1/2: 0.989 / Net I/σ(I): 10.61
Reflection shellResolution: 2.446→2.534 Å / Num. unique obs: 2390 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.446→48.293 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3176 1224 5 %
Rwork0.2608 --
obs0.2636 24476 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.446→48.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 33 23 4660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024695
X-RAY DIFFRACTIONf_angle_d0.4746358
X-RAY DIFFRACTIONf_dihedral_angle_d6.5222873
X-RAY DIFFRACTIONf_chiral_restr0.034761
X-RAY DIFFRACTIONf_plane_restr0.003813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.446-2.54380.46891320.35812519X-RAY DIFFRACTION98
2.5438-2.65960.40111370.32942581X-RAY DIFFRACTION100
2.6596-2.79980.38341340.30142554X-RAY DIFFRACTION100
2.7998-2.97520.37331360.29242593X-RAY DIFFRACTION100
2.9752-3.20490.35721360.29112585X-RAY DIFFRACTION100
3.2049-3.52730.31781370.28092607X-RAY DIFFRACTION100
3.5273-4.03750.32961260.28862400X-RAY DIFFRACTION92
4.0375-5.0860.28341400.21622652X-RAY DIFFRACTION100
5.086-100.26051460.21852761X-RAY DIFFRACTION99

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