[English] 日本語
Yorodumi
- PDB-9g4o: The strucuture of Streptococcus pyogenes GacA in complex with a f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g4o
TitleThe strucuture of Streptococcus pyogenes GacA in complex with a fragment
ComponentsdTDP-4-dehydrorhamnose reductase
KeywordsOXIDOREDUCTASE / GacA / Streptococcus / fragment
Function / homology
Function and homology information


: / dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-rhamnose biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYan, K. / Dorfmueller, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust225350/Z/22/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
CitationJournal: To Be Published
Title: Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Raimi, O. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6015
Polymers32,5361
Non-polymers1,0664
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-27 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.155, 45.702, 48.440
Angle α, β, γ (deg.)113.30, 99.54, 95.01
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein dTDP-4-dehydrorhamnose reductase


Mass: 32535.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: rmlD, SPy_0784 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9A0G6, dTDP-4-dehydrorhamnose reductase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-A1IH7 / 2-[4-(hydroxymethyl)phenyl]ethanoic acid


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate), 0.1 M MES/imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.545→43.411 Å / Num. obs: 21968 / % possible obs: 79.8 % / Redundancy: 3.1 % / CC1/2: 0.934 / Net I/σ(I): 5.4
Reflection shellResolution: 1.545→1.81 Å / Num. unique obs: 1098 / CC1/2: 0.547

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.41 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 1148 5.15 %
Rwork0.1818 --
obs0.1842 21968 54.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 72 163 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082418
X-RAY DIFFRACTIONf_angle_d0.9953301
X-RAY DIFFRACTIONf_dihedral_angle_d11.297330
X-RAY DIFFRACTIONf_chiral_restr0.053362
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.147560.228943X-RAY DIFFRACTION1
1.62-1.70.2472170.2615252X-RAY DIFFRACTION5
1.7-1.810.2429390.248744X-RAY DIFFRACTION15
1.81-1.950.31591170.23832166X-RAY DIFFRACTION45
1.95-2.140.28061840.2084195X-RAY DIFFRACTION86
2.14-2.450.25192310.19134579X-RAY DIFFRACTION95
2.45-3.090.22712690.18644630X-RAY DIFFRACTION96
3.09-43.410.19212850.15124534X-RAY DIFFRACTION95

+
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