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- PDB-7my0: Sy-CrtE IPP structure -

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Basic information

Entry
Database: PDB / ID: 7my0
TitleSy-CrtE IPP structure
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids
Function / homology
Function and homology information


dimethylallyltranstransferase / prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding / 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 / dimethylallyltranstransferase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPeat, T.S. / Newman, J.
Citation
Journal: Febs J. / Year: 2022
Title: Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase.
Authors: Satta, A. / Esquirol, L. / Ebert, B.E. / Newman, J. / Peat, T.S. / Plan, M. / Schenk, G. / Vickers, C.E.
#1: Journal: To Be Published
Title: Molecular characterization of cyanobacterial short-chain prenyltransferases
Authors: Peat, T.S. / Newman, J.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)67,73113
Polymers66,9522
Non-polymers77911
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-110 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.430, 73.643, 132.229
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-816-

HOH

21A-818-

HOH

31A-822-

HOH

41B-572-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase


Mass: 33476.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: crtE / Production host: Escherichia coli (E. coli) / References: UniProt: P72683
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein at 10 mg/mL was set up in 200 plus 200 nL drops with the reservoir as 20% (w/v) PEG 3350 and 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.37→47.06 Å / Num. obs: 122978 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.042 / Net I/σ(I): 9.2
Reflection shellResolution: 1.37→1.39 Å / Rmerge(I) obs: 2.746 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6040 / CC1/2: 0.52 / Rpim(I) all: 0.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7mxz

7mxz


Resolution: 1.37→43.93 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.065 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.16 6117 4.989 %
Rwork0.128 --
obs-122620 99.7 %
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: 16.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.038 Å20 Å2-0.134 Å2
2--1.303 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.37→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 42 621 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134795
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174633
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6416573
X-RAY DIFFRACTIONr_angle_other_deg1.6051.57510680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5925650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89122.298235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2371534
X-RAY DIFFRACTIONr_chiral_restr0.1120.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021052
X-RAY DIFFRACTIONr_nbd_refined0.2650.21268
X-RAY DIFFRACTIONr_nbd_other0.1980.277
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2413
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3921.4092495
X-RAY DIFFRACTIONr_mcbond_other2.3591.4072494
X-RAY DIFFRACTIONr_mcangle_it2.7242.1043180
X-RAY DIFFRACTIONr_mcangle_other2.7362.1063181
X-RAY DIFFRACTIONr_scbond_it3.6171.8652300
X-RAY DIFFRACTIONr_scbond_other3.6071.8632294
X-RAY DIFFRACTIONr_scangle_it4.2512.6433393
X-RAY DIFFRACTIONr_scangle_other4.252.6433394
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.0339428
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.41 Å
RfactorNum. reflection% reflection
Rfree0.333 450 -
Rwork0.294 8543 -
obs--98.98 %

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