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- PDB-9k9b: Apo form of Solanum tuberosum solanesyl diphosphate synthase -

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Basic information

Entry
Database: PDB / ID: 9k9b
TitleApo form of Solanum tuberosum solanesyl diphosphate synthase
ComponentsSolanesyl diphosphate synthase
KeywordsTRANSFERASE / chloroplast
Function / homology
Function and homology information


plastoquinone biosynthetic process / 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
Solanesyl diphosphate synthase
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.189 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: Apo form of Solanum tuberosum solanesyl diphosphate synthase
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

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Assembly

Deposited unit
A: Solanesyl diphosphate synthase
B: Solanesyl diphosphate synthase
C: Solanesyl diphosphate synthase
D: Solanesyl diphosphate synthase
E: Solanesyl diphosphate synthase
F: Solanesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)213,9156
Polymers213,9156
Non-polymers00
Water8,503472
1
A: Solanesyl diphosphate synthase
F: Solanesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)71,3052
Polymers71,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-19 kcal/mol
Surface area25080 Å2
MethodPISA
2
B: Solanesyl diphosphate synthase
D: Solanesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)71,3052
Polymers71,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-20 kcal/mol
Surface area25330 Å2
MethodPISA
3
C: Solanesyl diphosphate synthase
E: Solanesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)71,3052
Polymers71,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-20 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.694, 134.593, 101.045
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Solanesyl diphosphate synthase


Mass: 35652.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: 102593674 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1AAA6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, PEG 4000, MPD

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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: 2.189→44.725 Å / Num. obs: 101617 / % possible obs: 99.15 % / Redundancy: 10.429 % / CC1/2: 0.997 / Net I/σ(I): 10.95
Reflection shellResolution: 2.189→2.267 Å / Num. unique obs: 9744 / CC1/2: 0.692

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.189→44.725 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 5077 5 %
Rwork0.2012 --
obs0.2031 101501 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.189→44.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13729 0 0 472 14201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413906
X-RAY DIFFRACTIONf_angle_d0.55718779
X-RAY DIFFRACTIONf_dihedral_angle_d5.3518499
X-RAY DIFFRACTIONf_chiral_restr0.0362231
X-RAY DIFFRACTIONf_plane_restr0.0032421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1891-2.21390.31971520.23812897X-RAY DIFFRACTION89
2.2139-2.240.341690.29883208X-RAY DIFFRACTION99
2.24-2.26730.4071660.34633152X-RAY DIFFRACTION98
2.2673-2.2960.27851680.2393198X-RAY DIFFRACTION99
2.296-2.32620.26051680.21253183X-RAY DIFFRACTION100
2.3262-2.35810.25941740.19993312X-RAY DIFFRACTION100
2.3581-2.39180.23961670.20783172X-RAY DIFFRACTION100
2.3918-2.42750.27751690.20823212X-RAY DIFFRACTION100
2.4275-2.46540.28081710.22233239X-RAY DIFFRACTION100
2.4654-2.50580.32091690.22343219X-RAY DIFFRACTION100
2.5058-2.5490.22731690.21253203X-RAY DIFFRACTION100
2.549-2.59540.27331730.21883294X-RAY DIFFRACTION100
2.5954-2.64530.25271660.2153160X-RAY DIFFRACTION100
2.6453-2.69930.26541710.21223232X-RAY DIFFRACTION100
2.6993-2.75790.26111700.20833244X-RAY DIFFRACTION100
2.7579-2.82210.22611690.20783206X-RAY DIFFRACTION100
2.8221-2.89260.28581700.22353227X-RAY DIFFRACTION100
2.8926-2.97080.28921710.22233253X-RAY DIFFRACTION100
2.9708-3.05820.30471730.23183271X-RAY DIFFRACTION100
3.0582-3.15690.26581670.22693188X-RAY DIFFRACTION100
3.1569-3.26970.26371720.21243260X-RAY DIFFRACTION100
3.2697-3.40060.26261660.21923151X-RAY DIFFRACTION100
3.4006-3.55530.23251720.20433264X-RAY DIFFRACTION100
3.5553-3.74270.21461720.18653284X-RAY DIFFRACTION100
3.7427-3.9770.2131680.18243192X-RAY DIFFRACTION100
3.977-4.28390.23981710.1793243X-RAY DIFFRACTION100
4.2839-4.71450.20421720.16913258X-RAY DIFFRACTION100
4.7145-5.39570.22581720.19393267X-RAY DIFFRACTION100
5.3957-6.79420.24261690.21883226X-RAY DIFFRACTION100
6.7942-100.1531710.1533209X-RAY DIFFRACTION96

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