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- PDB-5ndy: crystal structure of variants -

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Basic information

Entry
Database: PDB / ID: 5ndy
Titlecrystal structure of variants
ComponentsGeranylgeranylglyceryl phosphate synthase
KeywordsTRANSFERASE / Methanobacterium thermoautotrophicum
Function / homology
Function and homology information


phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Geranylgeranylglyceryl phosphate synthase / GGGP/HepGP synthase group I / FMN-linked oxidoreductases / Geranylgeranylglyceryl phosphate synthase/Heptaprenylglyceryl phosphate synthase / GGGP/HepGP synthase superfamily / PcrB family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsLinde, M. / Rajendran, C. / Babinger, P. / Sterner, R.
CitationJournal: To Be Published
Title: crystal structure of variants from MtGGGPS
Authors: Sterner, R. / Babinger, P. / Linde, M. / Rajendran, C.
History
DepositionMar 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranylglyceryl phosphate synthase
B: Geranylgeranylglyceryl phosphate synthase
C: Geranylgeranylglyceryl phosphate synthase
D: Geranylgeranylglyceryl phosphate synthase
E: Geranylgeranylglyceryl phosphate synthase
F: Geranylgeranylglyceryl phosphate synthase


Theoretical massNumber of molelcules
Total (without water)166,0776
Polymers166,0776
Non-polymers00
Water9,890549
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-105 kcal/mol
Surface area50540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.539, 147.662, 90.347
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Geranylgeranylglyceryl phosphate synthase / MtGGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase


Mass: 27679.436 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: MTH_552 / Production host: Escherichia coli (E. coli)
References: UniProt: O26652, phosphoglycerol geranylgeranyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG, Tris Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→49.773 Å / Num. obs: 125165 / % possible obs: 97.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06882 / Rpim(I) all: 0.0283 / Rrim(I) all: 0.07452 / Net I/σ(I): 17.16
Reflection shellRmerge(I) obs: 1.068 / Rpim(I) all: 1.16 / Rrim(I) all: 0.4461

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2119: ???)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.949→49.773 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18
RfactorNum. reflection% reflection
Rfree0.2623 6257 5 %
Rwork0.2182 --
obs0.2204 125063 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.949→49.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10782 0 0 549 11331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710811
X-RAY DIFFRACTIONf_angle_d0.91814642
X-RAY DIFFRACTIONf_dihedral_angle_d14.3496494
X-RAY DIFFRACTIONf_chiral_restr0.0561668
X-RAY DIFFRACTIONf_plane_restr0.0061923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9493-1.97140.4622550.41731044X-RAY DIFFRACTION25
1.9714-1.99460.34672100.34633975X-RAY DIFFRACTION99
1.9946-2.01890.36392140.32444068X-RAY DIFFRACTION100
2.0189-2.04450.35642140.32014068X-RAY DIFFRACTION100
2.0445-2.07140.33492120.30924024X-RAY DIFFRACTION100
2.0714-2.09980.33012140.28684048X-RAY DIFFRACTION100
2.0998-2.12980.2952120.27154031X-RAY DIFFRACTION100
2.1298-2.16160.31292140.27064058X-RAY DIFFRACTION100
2.1616-2.19530.31712140.26964064X-RAY DIFFRACTION100
2.1953-2.23130.27772130.2574045X-RAY DIFFRACTION100
2.2313-2.26980.31622140.2624056X-RAY DIFFRACTION100
2.2698-2.31110.33412130.2574049X-RAY DIFFRACTION100
2.3111-2.35550.27712130.24954057X-RAY DIFFRACTION100
2.3555-2.40360.3142140.24594066X-RAY DIFFRACTION100
2.4036-2.45590.28472140.24854056X-RAY DIFFRACTION100
2.4559-2.5130.27992140.2534055X-RAY DIFFRACTION100
2.513-2.57580.31412130.24694059X-RAY DIFFRACTION100
2.5758-2.64550.31582120.24564033X-RAY DIFFRACTION100
2.6455-2.72330.28472150.25324073X-RAY DIFFRACTION100
2.7233-2.81120.27512140.23474061X-RAY DIFFRACTION100
2.8112-2.91170.29922150.25234084X-RAY DIFFRACTION100
2.9117-3.02820.2922140.23784071X-RAY DIFFRACTION100
3.0282-3.1660.28332130.24084047X-RAY DIFFRACTION100
3.166-3.33290.2622150.23174079X-RAY DIFFRACTION100
3.3329-3.54170.2572140.21084083X-RAY DIFFRACTION100
3.5417-3.81510.23582130.1964047X-RAY DIFFRACTION100
3.8151-4.19880.22392150.17724072X-RAY DIFFRACTION100
4.1988-4.8060.21312150.15824091X-RAY DIFFRACTION100
4.806-6.05330.22242170.18624111X-RAY DIFFRACTION100
6.0533-49.78960.22992180.18634131X-RAY DIFFRACTION100

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