[English] 日本語
Yorodumi
- PDB-2xme: The X-ray structure of CTP:inositol-1-phosphate cytidylyltransfer... -

+
Open data


ID or keywords:

Loading...

-
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 ...: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 1168 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 1.8 M SODIUM MALONATE PH 6.5 .

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more