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- PDB-5guf: Structural insight into an intramembrane enzyme for archaeal memb... -

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Basic information

Entry
Database: PDB / ID: 5guf
TitleStructural insight into an intramembrane enzyme for archaeal membrane lipids biosynthesis
ComponentsCDP-archaeol synthase
KeywordsTRANSFERASE / membrane protein / cars
Function / homology
Function and homology information


CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase / CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase activity / glycerophospholipid biosynthetic process / plasma membrane => GO:0005886
Similarity search - Function
CDP-archaeol synthase, archaea / CDP-archaeol synthase / CDP-archaeol synthase
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / CDP-archaeol synthase
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.397 Å
AuthorsCheng, W. / Ren, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: Cell Res. / Year: 2017
Title: Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes.
Authors: Ren, S. / Caforio, A. / Yang, Q. / Sun, B. / Yu, F. / Zhu, X. / Wang, J. / Dou, C. / Fu, Q. / Huang, N. / Sun, Q. / Nie, C. / Qi, S. / Gong, X. / He, J. / Wei, Y. / Driessen, A.J. / Cheng, W.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDP-archaeol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6366
Polymers19,0401
Non-polymers5955
Water1,33374
1
A: CDP-archaeol synthase
hetero molecules

A: CDP-archaeol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,27112
Polymers38,0812
Non-polymers1,19010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3960 Å2
ΔGint-66 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.505, 89.249, 98.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein CDP-archaeol synthase / CDP-2 / 3-bis-(O-geranylgeranyl)-sn-glycerol synthase


Mass: 19040.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: carS, APE_0433
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9YF05, CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.27 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 200mM NaCl, 20% (w/v) PEG 400, 100mM Tris/HCl pH 8.0

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9973 Å
DetectorType: DECTRIS PILATUS 300K / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9973 Å / Relative weight: 1
ReflectionResolution: 2.38→47.7 Å / Num. obs: 9961 / % possible obs: 98.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 37.701436451 Å2 / Net I/σ(I): 24.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2719)refinement
HKL-3000data processing
Aimlessdata reduction
XDSdata extraction
RefinementResolution: 2.397→44.625 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 995 9.99 %
Rwork0.2072 --
obs0.2114 9958 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→44.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 33 74 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021186
X-RAY DIFFRACTIONf_angle_d0.9941625
X-RAY DIFFRACTIONf_dihedral_angle_d11.496940
X-RAY DIFFRACTIONf_chiral_restr0.051199
X-RAY DIFFRACTIONf_plane_restr0.007205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3968-2.52320.30781250.23461148X-RAY DIFFRACTION90
2.5232-2.68130.25551470.20891258X-RAY DIFFRACTION99
2.6813-2.88830.25231320.19321281X-RAY DIFFRACTION100
2.8883-3.17880.21861410.18141297X-RAY DIFFRACTION100
3.1788-3.63860.19481500.1771294X-RAY DIFFRACTION100
3.6386-4.58360.26041460.19571312X-RAY DIFFRACTION100
4.5836-44.63220.26991540.24441373X-RAY DIFFRACTION99

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