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- PDB-4q2g: CRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL ... -

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Basic information

Entry
Database: PDB / ID: 4q2g
TitleCRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL FOR PHOSPHOLIPID BIOSYNTHESIS (S200C/S223C, inactive mutant)
ComponentsPhosphatidate cytidylyltransferase
KeywordsTRANSFERASE / intramembrane enzyme / CdsA fold / phospholipid biosynthesis lipid metabolism / CTP and phosphatidic acid binding / Nucleotidyltransferase / membrane
Function / homologyPhosphatidate cytidylyltransferase / Cytidylyltransferase family / Phosphatidate cytidylyltransferase signature. / phosphatidate cytidylyltransferase / phosphatidate cytidylyltransferase activity / CDP-diacylglycerol biosynthetic process / plasma membrane / : / Phosphatidate cytidylyltransferase
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsLiu, X. / Yin, Y. / Wu, J. / Liu, Z.
CitationJournal: Nat Commun / Year: 2014
Title: Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis
Authors: Liu, X. / Yin, Y. / Wu, J. / Liu, Z.
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Phosphatidate cytidylyltransferase
B: Phosphatidate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,11810
Polymers64,6542
Non-polymers1,4648
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-140 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.410, 141.410, 197.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Phosphatidate cytidylyltransferase / / CDP-DAG synthase / CDP-DG synthase / CDP-diacylglycerol synthase / CDS / CDP-diglyceride ...CDP-DAG synthase / CDP-DG synthase / CDP-diacylglycerol synthase / CDS / CDP-diglyceride pyrophosphorylase / CDP-diglyceride synthase / CTP:phosphatidate cytidylyltransferase


Mass: 32326.900 Da / Num. of mol.: 2 / Mutation: S220C, S278C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: cdsA, TM_1397 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q9X1B7, phosphatidate cytidylyltransferase
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.41 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8%-13% PEG3350, 100mM NaCl, 20mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00137 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2012 / Details: Mono-chromator and mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00137 Å / Relative weight: 1
ReflectionResolution: 3.4→28.1 Å / Num. all: 16348 / Num. obs: 16298 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.106 / Net I/σ(I): 11.1
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2345 / Rsym value: 0.673 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→28.1 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 7901259.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.315 821 5 %RANDOM
Rwork0.291 ---
all0.291 16348 --
obs0.291 16298 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.2693 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 117.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.32 Å20 Å20 Å2
2---13.32 Å20 Å2
3---26.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 3.4→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 48 0 4236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it1.58
X-RAY DIFFRACTIONc_mcangle_it2.9
X-RAY DIFFRACTIONc_scbond_it1.9
X-RAY DIFFRACTIONc_scangle_it2.36
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 135 5.1 %
Rwork0.406 2529 -
obs-2518 98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ctp_xplor_par.txtlhcII_bng_hglink.top
X-RAY DIFFRACTION5lhcII_bng_hglink.par

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