[English] 日本語
Yorodumi
- PDB-1ker: The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ker
TitleThe crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound
ComponentsdTDP-D-glucose 4,6-dehydratase
KeywordsLYASE / Rossmann fold
Function / homology
Function and homology information


dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / dTDP-rhamnose biosynthetic process / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic process / nucleotide binding
Similarity search - Function
dTDP-glucose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAllard, S.T.M. / Beis, K. / Giraud, M.-F. / Hegeman, A.D. / Gross, J.W. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Naismith, J.H.
CitationJournal: Structure / Year: 2002
Title: Toward a structural understanding of the dehydratase mechanism.
Authors: Allard, S.T. / Beis, K. / Giraud, M.F. / Hegeman, A.D. / Gross, J.W. / Wilmouth, R.C. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Maskell, D.J. / Naismith, J.H.
History
DepositionNov 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2002Provider: 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 1.4Aug 16, 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: dTDP-D-glucose 4,6-dehydratase
B: dTDP-D-glucose 4,6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7089
Polymers77,9652
Non-polymers2,7447
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-81 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.225, 96.151, 182.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein dTDP-D-glucose 4,6-dehydratase / E.C.4.2.1.46 / RmlB


Mass: 38982.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: rmlB / Variant: serotype 2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P95780, UniProt: Q8GIP9*PLUS, dTDP-glucose 4,6-dehydratase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 30% w/v PEG 8000, 0.1M sodium cacodylate pH 5.4, 0.2M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.6 mg/mlprotein1drop
22.5 mMdithiothreitol1drop
34 mMNAD+1drop
415 mMdTDP-D-glucose1drop
515 mMthymidine 5'-diphosphate1drop
630 %(w/v)PEG80001reservoir
70.2 Mammonium sulfate1reservoir
80.1 Msodium cacodylate1reservoirpH5.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→49.7 Å / Num. obs: 55517 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.232 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.112 / Net I/σ(I): 5.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8000 / Rsym value: 0.284 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 179806 / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 8000 / Num. measured obs: 26125 / Rmerge(I) obs: 0.284

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1G1A

1g1a


Resolution: 2.2→49.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 5507 9.9 %Random
Rwork0.175 ---
obs-55421 99.5 %-
Displacement parametersBiso mean: 17.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 175 712 6375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.2202
X-RAY DIFFRACTIONc_dihedral_angle_d22.1525
X-RAY DIFFRACTIONc_improper_angle_d0.7839
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection
Rfree0.218 500
Rwork0.189 -
obs-4950
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 49.7 Å / % reflection Rfree: 10 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1525
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7839
LS refinement shell
*PLUS
Rfactor Rfree: 0.218 / Rfactor Rwork: 0.189

+
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