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- PDB-4q7c: Structure of AF2299, a CDP-alcohol phosphotransferase -

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Basic information

Entry
Database: PDB / ID: 4q7c
TitleStructure of AF2299, a CDP-alcohol phosphotransferase
ComponentsAF2299, a CDP-alcohol phosphotransferase
KeywordsTRANSFERASE / CDP-alcohol phosphotransferase / membrane protein / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / metal ion binding / membrane
Similarity search - Function
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #30 / : / CDP-alcohol phosphatidyltransferase AF_2299-like, N-terminal / CDP-alcohol phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2G / Chem-MPG / L(+)-TARTARIC ACID / CDP-alcohol phosphatidyltransferase AF-2299-like N-terminal domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsClarke, O.B. / Sciara, G. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Shapiro, L. / Mancia, F. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for catalysis in a CDP-alcohol phosphotransferase.
Authors: Sciara, G. / Clarke, O.B. / Tomasek, D. / Kloss, B. / Tabuso, S. / Byfield, R. / Cohn, R. / Banerjee, S. / Rajashankar, K.R. / Slavkovic, V. / Graziano, J.H. / Shapiro, L. / Mancia, F.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _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 / _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: AF2299, a CDP-alcohol phosphotransferase
B: AF2299, a CDP-alcohol phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,78918
Polymers84,5212
Non-polymers4,26716
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-143 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.417, 90.852, 106.611
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AF2299, a CDP-alcohol phosphotransferase


Mass: 42260.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF2299, AF_2299 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: O27985
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-C2G / [CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER / CYTIDINE 5'-DIPHOSPHOGLYCEROL


Mass: 477.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N3O13P2

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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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7
Details: 15% PEG 550 MME, 0.1 M Na-HEPES pH 7.0, 0.2 M potassium sodium tartrate, 2.5 mM CDP-glycerol, 1 mM TCEP, Lipidic cubic phase (LCP), temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.0245 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0245 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. all: 31012 / Num. obs: 31012 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.98
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.1-3.290.6831.33198.8
3.29-3.520.4192.15199
3.52-3.80.2553.46198.9
3.8-4.160.1685.21198.7
4.16-4.650.1117.95197.7
4.65-5.360.1018.35198.4
5.36-6.560.1286.81198.2
6.56-9.230.05114.04198.4
9.230.02924.92197

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4O6M

4o6m


Resolution: 3.102→69.128 Å / SU ML: 0.46 / σ(F): 0.03 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1567 4.99 %
Rwork0.2376 --
obs0.2392 31397 99.75 %
all-31397 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.6475 Å2
Refinement stepCycle: LAST / Resolution: 3.102→69.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 140 0 5412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085530
X-RAY DIFFRACTIONf_angle_d0.6527456
X-RAY DIFFRACTIONf_dihedral_angle_d12.2321932
X-RAY DIFFRACTIONf_chiral_restr0.027885
X-RAY DIFFRACTIONf_plane_restr0.002906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1021-3.20220.34751530.33362623X-RAY DIFFRACTION100
3.2022-3.31670.32971540.31562786X-RAY DIFFRACTION100
3.3167-3.44950.3371490.29092650X-RAY DIFFRACTION100
3.4495-3.60650.30221160.26752794X-RAY DIFFRACTION100
3.6065-3.79660.32911400.24782724X-RAY DIFFRACTION100
3.7966-4.03440.29831660.2552646X-RAY DIFFRACTION100
4.0344-4.34590.23811390.22682746X-RAY DIFFRACTION100
4.3459-4.78310.27151260.22692737X-RAY DIFFRACTION99
4.7831-5.4750.29731250.23042690X-RAY DIFFRACTION100
5.475-6.89690.22061460.22562753X-RAY DIFFRACTION100
6.8969-69.14470.16991530.16072681X-RAY DIFFRACTION99

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