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- PDB-9hjz: Crystal structure of human geranylgeranyl diphosphate synthase mu... -

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Basic information

Entry
Database: PDB / ID: 9hjz
TitleCrystal structure of human geranylgeranyl diphosphate synthase mutant Y246D
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / Geranylgeranyl diphosphate / dimer / prenyltransferase
Function / homology
Function and homology information


isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / isoprenoid biosynthetic process ...isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranylgeranyl diphosphate synthase activity / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / nucleoplasm / metal ion binding / identical protein binding / cytosol / cytoplasm
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
CITRIC ACID / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsYehia, R. / Giladi, M. / Haitin, Y.
Funding support Israel, 8items
OrganizationGrant numberCountry
Israel Science Foundation1721/16 Israel
Israel Science Foundation1653/21 Israel
Other privateICRF 01214 Israel
Other privateICRF 19202 Israel
Other privateIsrael Cancer Association 20230029 Israel
Other privateKahn Foundation's Orion project Israel
Other privateKarl and Leonora Fingerhut Fund for Cancer Research Israel
Other privateRecanati Foundation Israel
CitationJournal: To Be Published
Title: Crystal structure of human geranylgeranyl diphosphate synthase mutant Y246D
Authors: Yehia, R. / Portasikova, J.M. / Kadek, A. / Man, P. / Giladi, M. / Haitin, Y.
History
DepositionDec 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9693
Polymers70,7762
Non-polymers1921
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-29 kcal/mol
Surface area24420 Å2
Unit cell
Length a, b, c (Å)192.731, 192.731, 97.635
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase / GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase ...GGPP synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase


Mass: 35388.195 Da / Num. of mol.: 2 / Mutation: Y246D
Source method: isolated from a genetically manipulated source
Details: Geranylgeranyl diphosphate synthase / Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95749, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 1.6M Sodium citrate tribasic dihydrate pH 6.5, 0.1M Trimethylamine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.54→46.855 Å / Num. obs: 35207 / % possible obs: 98.8 % / Redundancy: 12.4 % / CC1/2: 0.998 / Net I/σ(I): 14.55
Reflection shellResolution: 2.54→2.7 Å / Num. unique obs: 5555 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→46.85 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 1759 5 %
Rwork0.2223 --
obs0.2239 35165 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 13 34 4396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054455
X-RAY DIFFRACTIONf_angle_d0.626065
X-RAY DIFFRACTIONf_dihedral_angle_d18.6061559
X-RAY DIFFRACTIONf_chiral_restr0.039699
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.610.42591280.40922440X-RAY DIFFRACTION96
2.61-2.690.37931350.32312546X-RAY DIFFRACTION100
2.69-2.770.3021330.2832549X-RAY DIFFRACTION100
2.77-2.870.31071350.29082549X-RAY DIFFRACTION100
2.87-2.990.34641330.30852550X-RAY DIFFRACTION100
2.99-3.120.31841360.28012566X-RAY DIFFRACTION100
3.12-3.290.29541350.25542552X-RAY DIFFRACTION100
3.29-3.50.30841360.23552591X-RAY DIFFRACTION100
3.5-3.770.25931350.21592552X-RAY DIFFRACTION98
3.77-4.140.23741360.20272602X-RAY DIFFRACTION100
4.14-4.740.19791370.17512609X-RAY DIFFRACTION99
4.74-5.970.25321390.21512628X-RAY DIFFRACTION98
5.97-46.850.18951410.18432672X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5612-0.54541.57471.8527-1.84212.25870.0909-0.1218-0.26290.16450.03590.10040.0626-0.1189-0.19440.6702-0.04690.00270.4902-0.0460.6206-108.077914.857920.8584
21.7036-0.93030.34441.03250.33050.5739-0.032-0.0741-0.07350.16010.06880.1333-0.0855-0.1524-0.05340.6644-0.01290.0120.46550.01590.5473-110.443326.859627.907
37.27683.23961.49585.78810.43889.1890.1265-0.53810.5724-0.3682-0.14350.14860.0941-0.91630.28480.76580.14590.14750.50590.04810.5272-113.233534.877549.8997
43.2426-0.09692.52062.06640.3753.26630.0996-0.2439-0.20050.05160.05820.14550.5151-0.6236-0.13370.61090.03750.05050.56160.03770.6544-128.920625.061527.4098
51.76920.8176-1.63860.3855-0.71233.62790.1881-0.00560.1258-0.01650.0296-0.0216-0.32730.1241-0.20850.6932-0.03570.00230.5229-0.04780.5871-86.258130.680726.8567
62.95950.4825-0.6752.2736-0.72131.6325-0.0944-0.3089-0.50970.3083-0.1176-0.40250.05630.250.19790.6128-0.0421-0.01340.4712-0.02990.6063-74.200814.25721.9687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 296 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 296 )

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