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- PDB-2xmh: The X-ray structure of CTP:inositol-1-phosphate cytidylyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2xmh
TitleThe X-ray structure of CTP:inositol-1-phosphate cytidylyltransferase from Archaeoglobus fulgidus
ComponentsCTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
KeywordsTRANSFERASE / CDP-INOSITOL / DI-MYO-INOSITOL PHOSPHATE
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 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 ...: / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Bifunctional IPC transferase and DIPP synthase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsBrito, J.A. / Borges, N. / Vonrhein, C. / Santos, H. / Archer, M.
Citation
Journal: J. Bacteriol. / Year: 2011
Title: Crystal structure of Archaeoglobus fulgidus CTP:inositol-1-phosphate cytidylyltransferase, a key enzyme for di-myo-inositol-phosphate synthesis in (hyper)thermophiles.
Authors: Brito, J.A. / Borges, N. / Vonrhein, C. / Santos, H. / Archer, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Production, Crystallization and Preliminary X-Ray Analysis of Ctp:Inositol-1-Phosphate Cytidylyltransferase from Archaeoglobus Fulgidus.
Authors: Brito, J.A. / Borges, N. / Santos, H. / Archer, M.
History
DepositionJul 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
B: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
C: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
D: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
E: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
F: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,2929
Polymers157,7256
Non-polymers5673
Water3,675204
1
A: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
B: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7643
Polymers52,5752
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-8.1 kcal/mol
Surface area18190 Å2
MethodPISA
2
C: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
D: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7643
Polymers52,5752
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-10 kcal/mol
Surface area17770 Å2
MethodPISA
3
E: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
F: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7643
Polymers52,5752
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-10.2 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.680, 83.850, 127.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-2015-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9083, 0.4181, -0.01058), (0.4181, -0.9084, 0.003995), (-0.00794, -0.008052, -0.9999)1.683, -1.658, 313
2given(-0.4941, -0.5931, -0.6357), (-0.6177, -0.275, 0.7367), (-0.6118, 0.7567, -0.2305)99.08, -87.28, 164.8
3given(-0.8899, 0.3691, 0.2681), (0.3362, 0.1332, 0.9323), (0.3084, 0.9198, -0.2426)-30.36, -172.2, 221.9

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Components

#1: Protein
CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE


Mass: 26287.434 Da / Num. of mol.: 6 / Fragment: SOLUBLE DOMAIN, RESIDUES 55-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: DSMZ 7324 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O29976
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 1.2 M SODIUM CITRATE, 100 MM HEPES PH 8.2 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.067
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.067 Å / Relative weight: 1
ReflectionResolution: 2.4→48.28 Å / Num. obs: 64618 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 57.73 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.4→35.14 Å / Cor.coef. Fo:Fc: 0.8833 / Cor.coef. Fo:Fc free: 0.8527 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 3285 5.1 %RANDOM
Rwork0.2327 ---
obs0.2348 64587 98.8 %-
Displacement parametersBiso mean: 72.81 Å2
Baniso -1Baniso -2Baniso -3
1--8.4336 Å20 Å20 Å2
2---18.9854 Å20 Å2
3---27.4191 Å2
Refine analyzeLuzzati coordinate error obs: 0.444 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9598 0 39 204 9841
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019818HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2313222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3616SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes240HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1427HARMONIC5
X-RAY DIFFRACTIONt_it9818HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion21.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1249SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11212SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3135 253 5.31 %
Rwork0.2908 4510 -
all0.292 4763 -

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