[English] 日本語
Yorodumi
- PDB-1n2s: CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n2s
TitleCRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH
ComponentsdTDP-glucose oxidoreductase
KeywordsOXIDOREDUCTASE / ROSSMAN-FOLD / SUGAR-NUCLEOTIDE-BINDING DOMAIN
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / metal ion binding / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBlankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / Mcmiken, H.J. / Leonard, G.A. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H.
Citation
Journal: Structure / Year: 2002
Title: Variation on a Theme of SDR. dTDP-6-Deoxy-L- lyxo-4-Hexulose Reductase (RmlD) Shows a New Mg(2+)-Dependent Dimerization Mode
Authors: Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella ...Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella entrica serovar Typhimurim
Authors: Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Messner, P. / Whitfield, C. / Naismith, J.H.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 2000
Title: The rhamnose pathway
Authors: Giraud, M.F. / Naismith, J.H.
History
DepositionOct 24, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 1, 2002ID: 1KC0
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2013Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _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-glucose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4024
Polymers32,5901
Non-polymers8123
Water2,936163
1
A: dTDP-glucose oxidoreductase
hetero molecules

A: dTDP-glucose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8048
Polymers65,1802
Non-polymers1,6246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)47.435, 71.572, 82.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

MG

21A-902-

HOH

DetailsThe biological assembly is a dimer generated from the 2-fold crystallographic axis

-
Components

#1: Protein dTDP-glucose oxidoreductase / E.C.1.1.1.133 / DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE / DTDP-4-DEHYDRORHAMNOSE REDUCTASE / DTDP-4-KETO-L- ...DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE / DTDP-4-DEHYDRORHAMNOSE REDUCTASE / DTDP-4-KETO-L-RHAMNOSE REDUCTASE / DTDP-6-DEOXY-L-MANNOSE DEHYDROGENASE / DTDP-L-RHAMNOSE SYNTHETASE / RFBA PROTEIN / TDP-RHAMNOSE SYNTHETASE


Mass: 32589.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Species: Salmonella enterica / Strain: subsp. enterica serovar Typhimurium / Gene: RFBA / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDA DE3)PLYSS
References: UniProt: P26392, dTDP-4-dehydrorhamnose reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris, PEG 4000, MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→54.23 Å / Num. obs: 19137 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.7 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→81.7 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: TLS-OPTION WITH COFACTOR- BINDING, SUBSTRATE-BINDING DOMAINS AND WATERS AS THREE SEPARATE TLS-BODIES WAS USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.253 996 5.1 %RANDOM
Rwork0.199 ---
obs0.202 18528 99.7 %-
Displacement parametersBiso mean: 28.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2---3.95 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2→81.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 53 163 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.020.021
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.971
X-RAY DIFFRACTIONr_mcbond_it0.9211.5
X-RAY DIFFRACTIONr_mcangle_it1.5632
X-RAY DIFFRACTIONr_scbond_it2.4563
X-RAY DIFFRACTIONr_scangle_it3.5684.5
LS refinement shellResolution: 2→2.05 Å /
RfactorNum. reflection
Rfree0.289 65
Rwork0.27 -
obs-1368

+
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