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- PDB-9csl: Structure of mutant human geranylgeranyl pyrophosphate synthase (... -

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Basic information

Entry
Database: PDB / ID: 9csl
TitleStructure of mutant human geranylgeranyl pyrophosphate synthase (Y246D-C247L) in complex with isopentenyl pyrophosphate
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / Isopentenyl transferase / Isoprenyl synthase / Isoprenoid biosynthesis / Isoprenoids
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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEzekiel, S. / Park, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-04281 Canada
CitationJournal: Plos One / Year: 2025
Title: Engineering dimer mutants of human geranylgeranyl pyrophosphate synthase.
Authors: Ezekiel, S.J. / Searle, M. / Park, J.
History
DepositionJul 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,30716
Polymers74,8732
Non-polymers1,43414
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-173 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.110, 191.110, 96.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 296 / Label seq-ID: 23 - 318

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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: 37436.504 Da / Num. of mol.: 2 / Mutation: Y246D, C247L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Production host: Escherichia coli BL21(DE3) (bacteria)
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-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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium phosphate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→95.56 Å / Num. obs: 60724 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 40.173 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.023 / Rrim(I) all: 0.104 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 16.9 % / Rmerge(I) obs: 1.683 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2941 / CC1/2: 0.665 / Rpim(I) all: 0.419 / Rrim(I) all: 1.736 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→95.555 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.01 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3000 4.94 %Random
Rwork0.1785 57724 --
all0.18 ---
obs0.1803 60724 99.849 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.514 Å20.257 Å20 Å2
2--0.514 Å2-0 Å2
3----1.667 Å2
Refinement stepCycle: LAST / Resolution: 2.1→95.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 75 424 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164527
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.846550
X-RAY DIFFRACTIONr_angle_other_deg0.6151.76510418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.96523
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.43351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30510833
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.62910228
X-RAY DIFFRACTIONr_chiral_restr0.0910.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
X-RAY DIFFRACTIONr_nbd_refined0.2360.21226
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24190
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22423
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2394
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.225
X-RAY DIFFRACTIONr_nbd_other0.1850.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3820.217
X-RAY DIFFRACTIONr_mcbond_it4.624.8282317
X-RAY DIFFRACTIONr_mcbond_other4.6194.8282317
X-RAY DIFFRACTIONr_mcangle_it5.9728.6192898
X-RAY DIFFRACTIONr_mcangle_other5.9718.622899
X-RAY DIFFRACTIONr_scbond_it6.3245.4272508
X-RAY DIFFRACTIONr_scbond_other6.0535.3372461
X-RAY DIFFRACTIONr_scangle_it8.989.6943652
X-RAY DIFFRACTIONr_scangle_other8.8289.5423581
X-RAY DIFFRACTIONr_lrange_it10.46848.2475925
X-RAY DIFFRACTIONr_lrange_other10.37847.485789
X-RAY DIFFRACTIONr_ncsr_local_group_10.1410.058716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.140910.05006
12AX-RAY DIFFRACTIONLocal ncs0.140910.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1550.2741850.26542000.26544160.9470.94799.2980.248
2.155-2.2140.2822030.2440890.24242960.9480.9699.90690.218
2.214-2.2780.2832030.23540090.23842140.9430.96399.95250.207
2.278-2.3480.2192220.19538490.19640770.970.97599.85280.165
2.348-2.4250.2592180.18737420.1939650.9620.97899.87390.154
2.425-2.510.2241960.18436260.18738230.9680.97999.97380.151
2.51-2.6040.2291950.17635140.17837100.970.98199.9730.145
2.604-2.7110.2171700.17534140.17735860.9730.98399.94420.144
2.711-2.8310.2121710.17432600.17634350.9730.98299.88360.142
2.831-2.9690.21710.16731000.16932750.9750.98399.87790.141
2.969-3.130.2021710.17429770.17631490.9760.98299.96820.149
3.13-3.3190.2261410.17228310.17429720.9710.9831000.155
3.319-3.5480.2221220.17426860.17628120.9720.98499.85770.16
3.548-3.8320.1981100.16825110.16926250.9760.98599.84760.159
3.832-4.1970.1971290.15722960.15924250.9760.9861000.152
4.197-4.6910.1841000.1421080.14222100.9790.98899.90950.14
4.691-5.4150.1831050.15518580.15719660.9820.98699.84740.156
5.415-6.6270.243850.21716080.21816940.970.97799.9410.207
6.627-9.3490.21660.18612640.18713420.9780.98299.10580.201
9.349-95.5550.28370.2317820.2338220.9450.96599.6350.288

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