[English] 日本語
Yorodumi
- PDB-4arw: Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4arw
TitlePseudomonas aeruginosa RmlA in complex with allosteric inhibitor
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / biosynthetic process / nucleotide binding / metal ion binding
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
Chem-HNR / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsAlphey, M.S. / Pirrie, L. / Torrie, L.S. / Gardiner, M. / Westwood, N.J. / Gray, D. / Naismith, J.H.
CitationJournal: ACS Chem. Biol. / Year: 2013
Title: Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa.
Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / ...Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / Singh, M. / Gray, D. / Westwood, N.J. / Naismith, J.H.
History
DepositionApr 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Structure summary
Revision 1.2Dec 19, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Revision 1.3Mar 6, 2013Group: Database references
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.6Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf
Revision 1.7Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,68419
Polymers134,1324
Non-polymers2,55215
Water9,854547
1
A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules

A: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,64818
Polymers134,1324
Non-polymers2,51714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
2
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules

B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,71920
Polymers134,1324
Non-polymers2,58716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)63.990, 153.760, 134.650
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

21B-2058-

HOH

31C-2044-

HOH

41D-2062-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9553, 0.01008, 0.2955), (0.0137, 0.9999, 0.0102), (-0.2953, 0.01379, -0.9553)39.9, -20.59, 72.57
2given(0.999, -0.006691, -0.04455), (-0.006102, -0.9999, 0.01333), (-0.04464, -0.01305, -0.9989)5.643, -16.89, 68.22
3given(-0.9362, 0.008018, -0.3513), (-0.004666, -0.9999, -0.01039), (-0.3513, -0.008088, 0.9362)62.19, -35.53, 10.96

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE


Mass: 33532.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, 1L-myo-inositol 1-phosphate cytidylyltransferase

-
Non-polymers , 5 types, 562 molecules

#2: Chemical
ChemComp-HNR / N-(6-AMINO-1-BUTYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYL-BENZENESULFONAMIDE


Mass: 352.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H20N4O4S
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.55 Å3/Da / Density % sol: 51.71 % / Description: NONE
Crystal growpH: 6
Details: 4% PEG6000, 0.1M MES PH6, 0.05M MGCL2, 0.1M NABR, 1% B-ME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 18, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30.8 Å / Num. obs: 62911 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 79.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FZW

1fzw


Resolution: 2.204→30.815 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.124 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 3192 5.14 %RANDOM
Rwork0.175 ---
obs0.177 62911 96.134 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 35.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0.384 Å2
2---0.384 Å20 Å2
3----0.447 Å2
Refinement stepCycle: LAST / Resolution: 2.204→30.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9116 0 161 547 9824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.029500
X-RAY DIFFRACTIONr_bond_other_d0.0020.026417
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.99712904
X-RAY DIFFRACTIONr_angle_other_deg0.8643.00215532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00551166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23324.388433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.338151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3731554
X-RAY DIFFRACTIONr_chiral_restr0.0660.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021874
X-RAY DIFFRACTIONr_nbd_refined0.2150.22300
X-RAY DIFFRACTIONr_nbd_other0.1650.2106
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24610
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.024.0579499
X-RAY DIFFRACTIONr_mcbond_other0.5094.1716416
X-RAY DIFFRACTIONr_mcangle_it3.1736.03912900
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.39612.433210
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.07119.7727698
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 198 -
Rwork0.227 3530 -
obs--78.716 %

+
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