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- PDB-6jo3: Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate syn... -

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Basic information

Entry
Database: PDB / ID: 6jo3
TitleCrystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with substrate sn-glycerol-1-phosphate
ComponentsGeranylgeranylglyceryl phosphate synthase
KeywordsTRANSFERASE / ARCHAEA / ETHER LIPID / THERMOPLASMA / Structural Genomics
Function / homology
Function and homology information


phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / 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 / Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNemoto, N. / Miyazono, K. / Tanokura, M. / Yamagishi, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate.
Authors: Nemoto, N. / Miyazono, K.I. / Tanokura, M. / Yamagishi, A.
History
DepositionMar 20, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 3, 2019ID: 5B69
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,4562
Polymers27,2841
Non-polymers1721
Water72140
1
A: Geranylgeranylglyceryl phosphate synthase
hetero molecules

A: Geranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9124
Polymers54,5682
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3260 Å2
ΔGint-38 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.595, 105.595, 142.498
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

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Components

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


Mass: 27283.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: DSM 1728 / Gene: Ta0995 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HJH3, phosphoglycerol geranylgeranyltransferase
#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1 M sodium acetate pH 4.8 10% (w/v) polyethylene glycol 4000 10 mM rac-G1P 100 mM cesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.5 Å / Num. obs: 20203 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.988 / Net I/σ(I): 8.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1945 / CC1/2: 0.942 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mm1

4mm1


Resolution: 2.35→43.538 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.59
RfactorNum. reflection% reflection
Rfree0.2228 982 4.87 %
Rwork0.1985 --
obs0.1997 20163 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→43.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 10 40 1913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021904
X-RAY DIFFRACTIONf_angle_d0.5222573
X-RAY DIFFRACTIONf_dihedral_angle_d2.4971166
X-RAY DIFFRACTIONf_chiral_restr0.044299
X-RAY DIFFRACTIONf_plane_restr0.004329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3503-2.47420.30121170.27652691X-RAY DIFFRACTION100
2.4742-2.62920.3231520.26282659X-RAY DIFFRACTION100
2.6292-2.83220.25561400.23362686X-RAY DIFFRACTION100
2.8322-3.11710.30541440.23412709X-RAY DIFFRACTION100
3.1171-3.5680.24151390.22912734X-RAY DIFFRACTION100
3.568-4.49450.2021420.18262755X-RAY DIFFRACTION100
4.4945-43.5450.18331480.16472947X-RAY DIFFRACTION100
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)
10.41790.524-0.24421.9313-0.10161.6063-0.00580.2558-0.1922-0.5564-0.2985-0.17320.61420.0388-0.00770.58360.18050.07360.6875-0.02340.5833-30.6759-40.7584-11.0198
20.8809-0.149-0.79440.9518-0.65883.66410.0020.0389-0.03390.0223-0.263-0.1957-0.3870.09820.00060.5160.1015-0.03830.55450.01650.549-31.0014-30.49550.3459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 247 )

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