[English] 日本語
Yorodumi
- PDB-1g1l: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g1l
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-GLUCOSE COMPLEX.
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / L-rhamnose / nucleotidyltransferase / pyrophosphorylase / thymidylyltransferase / allostery
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / polysaccharide biosynthetic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / 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
CITRIC ACID / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77 Å
AuthorsBlankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naimsmith, J.H.
Citation
Journal: EMBO J. / Year: 2000
Title: The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Authors: Blankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Purification, Crystallisation and Preliminary Structural Characterization of Glucose-1-phosphate Thymidylyltransferase (RmlA), the First Enzyme of the dTDP-L-rhamnose Synthesis Pathway ...Title: The Purification, Crystallisation and Preliminary Structural Characterization of Glucose-1-phosphate Thymidylyltransferase (RmlA), the First Enzyme of the dTDP-L-rhamnose Synthesis Pathway from Pseudomonas aeruginosa
Authors: Blankenfeldt, W. / Giraud, M.F. / Leonard, G. / Rahim, R. / Creuzenet, C. / Lam, J.S. / Naismith, J.H.
#2: Journal: J.Biol.Chem. / Year: 1965
Title: The nucleotide specificity and feedback control of thymidine diphosphate D-glucose pyrophosphorylase
Authors: Melo, A. / Glaser, L.
History
DepositionOct 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2012Group: Atomic model / Refinement description
Revision 1.4Jan 31, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_residues / Item: _citation_author.name
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,53449
Polymers259,9118
Non-polymers11,62341
Water53,5232971
1
A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,91125
Polymers129,9554
Non-polymers5,95621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23790 Å2
ΔGint-285 kcal/mol
Surface area41000 Å2
MethodPISA
2
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,62324
Polymers129,9554
Non-polymers5,66720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22890 Å2
ΔGint-264 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.575, 73.410, 134.290
Angle α, β, γ (deg.)89.94, 80.61, 80.93
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer best described as a dimer of dimers.

-
Components

#1: Protein
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE / GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA)


Mass: 32488.844 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DAU / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE


Mass: 564.329 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2971 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 9-11 % (w/v) PEG 6000, 0.5 M lithium sulfate, 0.1 M citrate. 4 + 4 mikrolitre. Substrate added in 1 mikrolitre 50 mM., pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 293 K
Details: Blankenfeldt, W., (2000) Acta Crystallogr.,Sect.D, 56, 1501.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-12 %(w/v)PEG60001reservoir
20.5 Mlithium sulfate1reservoir
30.1 Mcitrate/NaOH1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.77→40.64 Å / Num. obs: 202988 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.1
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.302 / % possible all: 77.4
Reflection
*PLUS
Num. measured all: 483036
Reflection shell
*PLUS
% possible obs: 77.4 % / Mean I/σ(I) obs: 2.4

-
Processing

Software
NameVersionClassification
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.77→40.64 Å / SU B: 7.97272 / SU ML: 0.12873 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.25383 / ESU R Free: 0.12348 / Stereochemistry target values: Engh and Huber
Details: TLS refinement in REFMAC5. Anisotropic B-factors calculated but not refined
RfactorNum. reflection% reflectionSelection details
Rfree0.215 12192 5 %RANDOM
Rwork0.156 ---
obs0.159 230146 93.3 %-
Displacement parametersBiso mean: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.02 Å2-0.03 Å2
2---0.16 Å2-0.26 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.77→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18296 0 717 2971 21984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_mcbond_it4.271.5
X-RAY DIFFRACTIONp_mcangle_it5.7082
X-RAY DIFFRACTIONp_scbond_it6.1383
X-RAY DIFFRACTIONp_scangle_it7.6784.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1260.2
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.38
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / Rfactor Rwork: 0.247

+
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