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- PDB-4mnd: Crystal structure of Archaeoglobus fulgidus IPCT-DIPPS bifunction... -

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Basic information

Entry
Database: PDB / ID: 4mnd
TitleCrystal structure of Archaeoglobus fulgidus IPCT-DIPPS bifunctional membrane protein
ComponentsCTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase
KeywordsTRANSFERASE / Transmembrane protein / Rossmann Fold / CDP-alcohol phosphotransferase
Function / homology
Function and homology information


1L-myo-inositol 1-phosphate cytidylyltransferase / CDP-L-myo-inositol myo-inositolphosphotransferase / phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotidyltransferase activity / membrane / metal ion binding
Similarity search - Function
: / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...: / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
EICOSANE / Bifunctional IPC transferase and DIPP synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsNogly, P. / Gushchin, I. / Remeeva, A. / Esteves, A.M. / Ishchenko, A. / Ma, P. / Grudinin, S. / Borges, N. / Round, E. / Moraes, I. ...Nogly, P. / Gushchin, I. / Remeeva, A. / Esteves, A.M. / Ishchenko, A. / Ma, P. / Grudinin, S. / Borges, N. / Round, E. / Moraes, I. / Borshchevskiy, V. / Santos, H. / Gordeliy, V. / Archer, M.
CitationJournal: Nat Commun / Year: 2014
Title: X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism.
Authors: Nogly, P. / Gushchin, I. / Remeeva, A. / Esteves, A.M. / Borges, N. / Ma, P. / Ishchenko, A. / Grudinin, S. / Round, E. / Moraes, I. / Borshchevskiy, V. / Santos, H. / Gordeliy, V. / Archer, M.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 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_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_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7876
Polymers53,6321
Non-polymers1,1545
Water1629
1
A: CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase
hetero molecules

A: CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,57412
Polymers107,2652
Non-polymers2,30910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area6250 Å2
ΔGint-54 kcal/mol
Surface area36370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.369, 107.584, 123.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase / Bifunctional IPC transferase and DIPP synthase


Mass: 53632.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0263 / Production host: Escherichia coli (E. coli)
References: UniProt: O29976, 1L-myo-inositol 1-phosphate cytidylyltransferase, CDP-L-myo-inositol myo-inositolphosphotransferase
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 295 K / pH: 7
Details: PEG, sodium malonate, pH 7, in meso crystallization, temperature 22K, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.65→61.82 Å / Num. obs: 15952 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XME

2xme


Resolution: 2.66→53.85 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.848 / SU B: 29.957 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30006 838 5 %RANDOM
Rwork0.24281 ---
obs0.24561 15813 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.311 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å2-0 Å2-0 Å2
2--4.09 Å20 Å2
3----6.53 Å2
Refinement stepCycle: LAST / Resolution: 2.66→53.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 39 9 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193203
X-RAY DIFFRACTIONr_bond_other_d0.0020.023167
X-RAY DIFFRACTIONr_angle_refined_deg0.5961.9724319
X-RAY DIFFRACTIONr_angle_other_deg0.50437239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0465406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19822.846123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7471521
X-RAY DIFFRACTIONr_chiral_restr0.0380.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023538
X-RAY DIFFRACTIONr_gen_planes_other00.02721
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.657→2.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 67 -
Rwork0.331 1124 -
obs--98.43 %
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)
13.74051.88280.08656.05690.13268.2245-0.26230.7362-0.1367-0.55810.79460.32960.1165-0.6688-0.53220.08830.0177-0.03950.655-0.00650.406725.493226.215679.0078
23.17190.55021.03910.23890.16933.8903-0.13880.7125-0.048-0.11950.11540.147-0.3993-0.130.02340.1275-0.0234-0.06040.372-0.02010.325424.196328.306979.1969
32.5332-1.4416-1.49996.8159-2.28936.02890.08360.5646-0.19140.19650.1905-0.1073-0.0670.6064-0.27420.06540.011-0.08260.6727-0.12280.345842.315724.341881.8839
44.6375-1.3416-1.00930.70050.3750.256-0.13120.7681-0.524-0.04140.1066-0.0310.0554-0.05260.02470.18670.0019-0.07130.6641-0.31180.347541.487713.197374.6823
52.69661.8242.94444.35540.20446.51980.2960.3324-0.3504-0.5433-0.37130.18810.33320.65620.07530.33290.0747-0.19490.6094-0.20360.386630.682818.048664.1915
62.9566-1.4488-0.63961.25141.62745.4895-0.12270.2113-0.20470.16550.14820.09310.40780.4561-0.02550.057-0.0142-0.00650.2381-0.04340.404137.27620.838790.2479
79.72112.89536.29852.12281.58116.51740.01240.59840.04560.16910.0451-0.42880.23160.6142-0.05750.20140.019-0.01610.07250.01130.38642.056428.6883108.8187
82.66690.62212.30583.71671.32937.01260.1947-0.20130.09940.8563-0.23930.00730.2303-0.69690.04460.2067-0.04680.05050.0732-0.00380.387832.180134.8995118.9308
94.59351.4277-1.68331.355-1.308326.3679-0.02090.15460.39390.1376-0.2684-0.1182-0.21870.37430.28930.0806-0.0287-0.03190.13940.03860.348734.564134.0588102.6233
101.39720.83420.57123.60640.50440.30280.13350.0702-0.09850.4551-0.0794-0.31680.12320.0895-0.05410.190.0476-0.04630.08270.00210.416545.796846.009118.3596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 89
2X-RAY DIFFRACTION2A90 - 175
3X-RAY DIFFRACTION3A176 - 198
4X-RAY DIFFRACTION4A199 - 230
5X-RAY DIFFRACTION5A231 - 260
6X-RAY DIFFRACTION6A261 - 291
7X-RAY DIFFRACTION7A295 - 316
8X-RAY DIFFRACTION8A317 - 355
9X-RAY DIFFRACTION9A356 - 369
10X-RAY DIFFRACTION10A370 - 489

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