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

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Basic information

Entry
Database: PDB / ID: 2xme
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
Bifunctional IPC transferase and DIPP synthase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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
G: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
H: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
I: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
J: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
K: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
L: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,18620
Polymers315,44912
Non-polymers7378
Water21,0421168
1
A: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
B: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7594
Polymers52,5752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-8.8 kcal/mol
Surface area18440 Å2
MethodPISA
2
C: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
D: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7594
Polymers52,5752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-8.3 kcal/mol
Surface area18430 Å2
MethodPISA
3
E: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
F: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6673
Polymers52,5752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-12 kcal/mol
Surface area18350 Å2
MethodPISA
4
G: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
H: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6673
Polymers52,5752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8.4 kcal/mol
Surface area18240 Å2
MethodPISA
5
I: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
J: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6673
Polymers52,5752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-7.7 kcal/mol
Surface area18360 Å2
MethodPISA
6
K: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
L: CTP-INOSITOL-1-PHOSPHATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6673
Polymers52,5752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-11.1 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.030, 127.550, 141.480
Angle α, β, γ (deg.)90.00, 90.56, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5212, -0.002139, -0.8534), (-0.00218, -1, 0.003838), (-0.8534, 0.003861, 0.5212)130.6, -220.4, 73.92
2given(-0.6742, 0.4895, 0.553), (0.52, -0.2171, 0.8261), (0.5244, 0.8445, -0.1082)172.1, -151.9, 38.82
3given(-0.4346, -0.6485, -0.625), (-0.7026, -0.1901, 0.6857), (-0.5635, 0.7371, -0.373)49.16, -98.41, 157.7
4given(-0.8621, 0.009633, 0.5067), (-0.009207, -1, 0.003345), (0.5067, -0.001782, 0.8621)43.58, -89.95, -11.88
5given(0.1575, -0.9374, 0.3106), (-0.9484, -0.2312, -0.2169), (0.2752, -0.2605, -0.9254)-3.393, 27.54, 101.1
6given(0.234, 0.9718, 0.03026), (0.9722, -0.2341, 0.000134), (0.007214, 0.02939, -0.9995)70.34, -89.27, 17.61

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Components

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


Mass: 26287.434 Da / Num. of mol.: 12 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1168 / 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: 2.47 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 1.8 M SODIUM MALONATE PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.89→142.49 Å / Num. obs: 219870 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 30.36 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / % possible all: 83

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMH

2xmh


Resolution: 1.89→27.67 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 10915 5.02 %RANDOM
Rwork0.206 ---
obs0.208 217329 --
Displacement parametersBiso mean: 45.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.1418 Å20 Å25.7576 Å2
2--5.703 Å20 Å2
3----5.8448 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.89→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19186 0 48 1168 20402
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119618HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.126409HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7154SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes483HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2840HARMONIC5
X-RAY DIFFRACTIONt_it19618HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2507SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22541SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 596 4.89 %
Rwork0.3507 11603 -
all0.3523 12199 -
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)
11.9211.1998-0.04513.8499-0.41781.09240.0681-0.1111-0.10980.7646-0.1064-0.06950.0263-0.01280.03830.2357-0.01470.177-0.2297-0.0057-0.197681.1243-119.79436.4174
21.151-0.04380.27342.91011.47522.55540.02910.07930.10770.2216-0.26860.61710.1108-0.18410.2395-0.0359-0.0050.3072-0.2184-0.0190.078957.5917-100.27722.9182
31.5940.5659-0.46133.6501-0.68691.13280.1536-0.04420.12340.4924-0.00910.3568-0.1656-0.0001-0.14450.19210.00290.1886-0.1793-0.0143-0.181974.0273-65.279514.0936
41.3302-0.8084-0.50333.03080.66853.48960.10430.1263-0.0622-0.1405-0.1483-0.2448-0.37570.34610.0440.0726-0.07240.0427-0.14710.0132-0.166598.2243-87.704820.0534
50.9803-0.44860.29152.0104-0.50440.69550.05940.0924-0.0262-0.33480.01950.15530.1114-0.0181-0.07890.1958-0.02750.124-0.1161-0.0088-0.151934.2177-89.84253.8073
61.25130.7323-0.11064.0498-0.06241.95930.0294-0.1381-0.03360.2739-0.1446-0.47740.19290.32820.11520.0645-0.00770.1764-0.15570.0159-0.146258.9784-68.337753.8835
71.5819-0.6584-0.12742.7961-0.56310.88330.11870.0978-0.0089-0.532-0.0387-0.01250.0052-0.0871-0.08010.2448-0.03010.2034-0.1812-0.0182-0.181446.7471-35.289734.3259
81.4026-0.3489-0.50934.09811.09821.56960.05890.07460.0489-0.5748-0.09020.5131-0.0823-0.1330.03130.1142-0.036-0.063-0.22040.0213-0.089120.2419-54.525941.5621
90.5567-0.4132-0.34183.03861.06321.60470.0080.0137-0.0469-0.3772-0.02830.0081-0.3154-0.06890.02020.12-0.01080.1602-0.15110.0082-0.089340.6305-0.153252.1243
101.78230.57440.48153.2956-0.54852.78160.0646-0.20770.07980.1773-0.13550.2938-0.0498-0.15220.0708-0.1066-0.01330.1448-0.1502-0.0292-0.002819.619-22.439764.9547
112.7681-0.9613-1.78354.5862-0.26523.48670.03030.4928-0.4522-0.4191-0.46220.49260.1547-0.40790.4319-0.16220.02080.1285-0.1647-0.15050.009162.7569-5.0323-0.1254
120.81670.0935-0.413.00590.41811.8781-0.01830.03350.06070.22680.00240.05640.0721-0.04310.01580.104-0.01710.2938-0.1985-0.0122-0.054979.6143-27.619117.6214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)
5X-RAY DIFFRACTION5(CHAIN E)
6X-RAY DIFFRACTION6(CHAIN F)
7X-RAY DIFFRACTION7(CHAIN G)
8X-RAY DIFFRACTION8(CHAIN H)
9X-RAY DIFFRACTION9(CHAIN I)
10X-RAY DIFFRACTION10(CHAIN J)
11X-RAY DIFFRACTION11(CHAIN K)
12X-RAY DIFFRACTION12(CHAIN L)

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