[English] 日本語
Yorodumi
- PDB-8fv8: E coli. CTP synthase in complex with dF-dCTP + ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fv8
TitleE coli. CTP synthase in complex with dF-dCTP + ADP
ComponentsCTP synthaseCTP synthetase
KeywordsCYTOSOLIC PROTEIN / LIGASE / Inhibitor complex / Metabolic enzyme
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / glutaminase activity / glutamine metabolic process / ATP binding / metal ion binding
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-GTF / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHolyoak, T. / McLeod, M.J. / Tran, N.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR)114895 Canada
CitationJournal: Protein Sci. / Year: 2023
Title: A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate.
Authors: McLeod, M.J. / Tran, N. / McCluskey, G.D. / Gillis, T.D. / Bearne, S.L. / Holyoak, T.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: CTP synthase
BBB: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8018
Polymers120,8942
Non-polymers1,9076
Water9,872548
1
AAA: CTP synthase
BBB: CTP synthase
hetero molecules

AAA: CTP synthase
BBB: CTP synthase
hetero molecules


  • defined by author&software
  • 246 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)245,60116
Polymers241,7884
Non-polymers3,81312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16550 Å2
ΔGint-125 kcal/mol
Surface area72660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.014, 109.426, 129.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-960-

HOH

-
Components

#1: Protein CTP synthase / CTP synthetase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTPS / UTP--ammonia ligase


Mass: 60446.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrG, ECS88_3048 / Plasmid: pET-15B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B7MLA1, CTP synthase (glutamine hydrolysing)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GTF / 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) / Gemcitabine-TRIPHOSPHATE


Mass: 503.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14F2N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.6534 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6534 Å / Relative weight: 1
ReflectionResolution: 2.05→83.5 Å / Num. obs: 140206 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 12.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.567 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 13859 / CC1/2: 0.749 / CC star: 0.925 / Rpim(I) all: 0.749 / Rrim(I) all: 1.641 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKV

5tkv


Resolution: 2.05→83.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.352 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2159 6950 4.962 %
Rwork0.1973 133116 -
all0.198 --
obs-140066 99.766 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.504 Å20 Å2-0 Å2
2--0.396 Å2-0 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 2.05→83.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 116 548 8998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138854
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158436
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.64312071
X-RAY DIFFRACTIONr_angle_other_deg1.1551.57719429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98922.056462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.548151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8551566
X-RAY DIFFRACTIONr_chiral_restr0.0530.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021988
X-RAY DIFFRACTIONr_nbd_refined0.1770.21689
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.28381
X-RAY DIFFRACTIONr_nbtor_refined0.1470.24192
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.24128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2597
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.225
X-RAY DIFFRACTIONr_nbd_other0.1480.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.233
X-RAY DIFFRACTIONr_mcbond_it1.2263.9954371
X-RAY DIFFRACTIONr_mcbond_other1.2263.9954370
X-RAY DIFFRACTIONr_mcangle_it2.1345.9795488
X-RAY DIFFRACTIONr_mcangle_other2.1345.985489
X-RAY DIFFRACTIONr_scbond_it1.1764.174483
X-RAY DIFFRACTIONr_scbond_other1.1764.174484
X-RAY DIFFRACTIONr_scangle_it2.0486.1866573
X-RAY DIFFRACTIONr_scangle_other2.0486.1866574
X-RAY DIFFRACTIONr_lrange_it5.29947.429776
X-RAY DIFFRACTIONr_lrange_other5.17847.0249635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.2954990.299785X-RAY DIFFRACTION99.9903
2.103-2.1610.2865410.2649442X-RAY DIFFRACTION99.9399
2.161-2.2240.2664570.2579326X-RAY DIFFRACTION99.9796
2.224-2.2920.2614790.2459012X-RAY DIFFRACTION99.9684
2.292-2.3670.2624780.2358644X-RAY DIFFRACTION99.9671
2.367-2.450.2364120.2338481X-RAY DIFFRACTION99.9775
2.45-2.5430.2364140.228216X-RAY DIFFRACTION99.919
2.543-2.6460.2463860.2247895X-RAY DIFFRACTION99.9276
2.646-2.7640.2554040.2217513X-RAY DIFFRACTION99.9117
2.764-2.8990.2313810.2157203X-RAY DIFFRACTION99.9078
2.899-3.0560.2483580.2226902X-RAY DIFFRACTION99.9587
3.056-3.2410.2233440.2076524X-RAY DIFFRACTION99.7241
3.241-3.4650.2223020.1966123X-RAY DIFFRACTION99.5815
3.465-3.7420.193000.185722X-RAY DIFFRACTION99.5207
3.742-4.0990.1842810.1635251X-RAY DIFFRACTION99.4964
4.099-4.5820.1722770.1394771X-RAY DIFFRACTION99.331
4.582-5.2910.1682220.154237X-RAY DIFFRACTION99.4425
5.291-6.4780.1711890.1833605X-RAY DIFFRACTION99.2414
6.478-9.1530.1961410.1732860X-RAY DIFFRACTION99.2722
9.153-83.50.285850.2471604X-RAY DIFFRACTION96.1298
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)
10.4093-0.2210.05910.24070.21810.66020.04120.1219-0.0241-0.0816-0.19840.0707-0.0916-0.18310.15720.05260.104-0.02940.2304-0.05390.044955.820912.51336.4583
20.49680.1482-0.1520.1219-0.09150.39360.0341-0.05630.04920.058-0.08020.04570.0326-0.03740.04620.0528-0.07580.03810.1144-0.04870.03853.9597-7.894286.1385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 543
2X-RAY DIFFRACTION2ALLBBB1 - 543

+
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