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- PDB-4jej: GGGPS from Flavobacterium johnsoniae -

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Basic information

Entry
Database: PDB / ID: 4jej
TitleGGGPS from Flavobacterium johnsoniae
ComponentsGeranylgeranylglyceryl phosphate synthase
KeywordsTRANSFERASE / PcrB-like / FsPP / GGPP
Function / homology
Function and homology information


phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / imidazoleglycerol-phosphate synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Geranylgeranylglyceryl phosphate synthase / 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
SN-GLYCEROL-1-PHOSPHATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPeterhoff, D. / Beer, B. / Rajendran, C. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization.
Authors: Peterhoff, D. / Beer, B. / Rajendran, C. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9896
Polymers26,5241
Non-polymers4665
Water3,261181
1
A: Geranylgeranylglyceryl phosphate synthase
hetero molecules

A: Geranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,97912
Polymers53,0472
Non-polymers93210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area4990 Å2
ΔGint-75 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.270, 43.010, 75.927
Angle α, β, γ (deg.)90.00, 117.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Geranylgeranylglyceryl phosphate synthase


Mass: 26523.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_1584 / Plasmid: pET 21a / Production host: Escherichia coli (E. coli) / References: UniProt: A5FJK8

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→37.06 Å / Num. obs: 34719 / % possible obs: 95.9 % / Observed criterion σ(I): 2.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6X and 1VIZ

2f6x

1viz


Resolution: 1.52→37.06 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1732 5 %
Rwork0.177 --
obs0.178 34657 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 27 181 2014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011855
X-RAY DIFFRACTIONf_angle_d1.2572523
X-RAY DIFFRACTIONf_dihedral_angle_d12.897675
X-RAY DIFFRACTIONf_chiral_restr0.069310
X-RAY DIFFRACTIONf_plane_restr0.006318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5243-1.56920.3516950.321830X-RAY DIFFRACTION65
1.5692-1.61990.331460.27382781X-RAY DIFFRACTION97
1.6199-1.67780.25061470.25452783X-RAY DIFFRACTION98
1.6778-1.74490.241460.21842784X-RAY DIFFRACTION98
1.7449-1.82430.21961480.18262820X-RAY DIFFRACTION99
1.8243-1.92050.21981470.18382794X-RAY DIFFRACTION98
1.9205-2.04080.21161480.1762811X-RAY DIFFRACTION99
2.0408-2.19840.21171490.16142819X-RAY DIFFRACTION99
2.1984-2.41960.18191500.16792863X-RAY DIFFRACTION99
2.4196-2.76960.19641500.1722838X-RAY DIFFRACTION99
2.7696-3.4890.17691500.16972849X-RAY DIFFRACTION98
3.489-37.0720.16841560.15852953X-RAY DIFFRACTION100

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