[English] 日本語
Yorodumi
- PDB-5a04: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a04
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with glucose
ComponentsALDOSE-ALDOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / 1,4-DIETHYLENE DIOXIDE / Chem-NDP / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsTaberman, H. / Rouvinen, J. / Parkkinen, T.
CitationJournal: Biochem.J. / Year: 2015
Title: Structure and Function of Caulobacter Crescentus Aldose-Aldose Oxidoreductase.
Authors: Taberman, H. / Andberg, M. / Koivula, A. / Hakulinen, N. / Penttila, M. / Rouvinen, J. / Parkkinen, T.
History
DepositionApr 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALDOSE-ALDOSE OXIDOREDUCTASE
B: ALDOSE-ALDOSE OXIDOREDUCTASE
C: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,84732
Polymers223,7376
Non-polymers7,11126
Water36,6972037
1
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,97911
Polymers74,5792
Non-polymers2,4009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-10.2 kcal/mol
Surface area30540 Å2
MethodPQS
2
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6228
Polymers74,5792
Non-polymers2,0436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-4 kcal/mol
Surface area30430 Å2
MethodPQS
3
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,24713
Polymers74,5792
Non-polymers2,66811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-5.6 kcal/mol
Surface area30760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.154, 153.516, 108.145
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0582, -0.8208, 0.5682), (0.8202, -0.3638, -0.4415), (0.5692, 0.4403, 0.6944)24.7202, -9.0866, -19.2203
2given(0.2317, -0.6735, -0.7019), (-0.7525, -0.5813, 0.3095), (-0.6165, 0.4565, -0.6415)70.7227, 25.4875, 64.1654
3given(0.1894, 0.7466, -0.6377), (0.6548, -0.58, -0.4846), (-0.7317, -0.3258, -0.5988)59.0551, -2.2274, 67.4522
4given(-0.9868, 0.1619, -0.0001), (0.1581, 0.9638, -0.2148), (-0.0347, -0.212, -0.9767)84.7287, -1.6421, 47.5206
5given(-0.3355, 0.5619, 0.7561), (-0.5587, -0.7649, 0.3206), (0.7585, -0.3149, 0.5706)18.1289, 20.5301, -22.4607

-
Components

-
Protein / Sugars , 2 types, 15 molecules ABCDEF

#1: Protein
ALDOSE-ALDOSE OXIDOREDUCTASE


Mass: 37289.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS CB15 (bacteria) / Strain: CB15 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q9A8X3*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 2054 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2037 / 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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6.5 / Details: MES PH 6.5, AMMONIUM SULPHATE, DIOXANE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 338561 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6A

1h6a


Resolution: 1.698→47.591 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 16929 5 %
Rwork0.1594 --
obs0.1604 338561 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.698→47.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15558 0 456 2037 18051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716385
X-RAY DIFFRACTIONf_angle_d1.10922262
X-RAY DIFFRACTIONf_dihedral_angle_d12.726097
X-RAY DIFFRACTIONf_chiral_restr0.0472430
X-RAY DIFFRACTIONf_plane_restr0.0052898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.698-1.71730.35795080.33439638X-RAY DIFFRACTION89
1.7173-1.73750.31085620.293710688X-RAY DIFFRACTION99
1.7375-1.75860.27955640.267210715X-RAY DIFFRACTION99
1.7586-1.78090.26855640.245510706X-RAY DIFFRACTION99
1.7809-1.80430.25235660.227810757X-RAY DIFFRACTION99
1.8043-1.82910.25725620.216410672X-RAY DIFFRACTION99
1.8291-1.85520.2185640.197410721X-RAY DIFFRACTION99
1.8552-1.88290.21975660.18810749X-RAY DIFFRACTION99
1.8829-1.91230.2295630.190710701X-RAY DIFFRACTION99
1.9123-1.94370.22325630.190610706X-RAY DIFFRACTION99
1.9437-1.97720.2115610.188610653X-RAY DIFFRACTION99
1.9772-2.01310.21875660.186810745X-RAY DIFFRACTION100
2.0131-2.05190.20535640.170110734X-RAY DIFFRACTION99
2.0519-2.09370.17895650.160910727X-RAY DIFFRACTION99
2.0937-2.13930.17515670.159610777X-RAY DIFFRACTION99
2.1393-2.1890.19485690.157410799X-RAY DIFFRACTION100
2.189-2.24380.16965680.152910790X-RAY DIFFRACTION100
2.2438-2.30440.1715640.15310733X-RAY DIFFRACTION100
2.3044-2.37220.18165670.156310772X-RAY DIFFRACTION100
2.3722-2.44880.18785670.154610767X-RAY DIFFRACTION100
2.4488-2.53630.18515650.158310730X-RAY DIFFRACTION99
2.5363-2.63790.19955700.160510831X-RAY DIFFRACTION100
2.6379-2.75790.17255690.155910818X-RAY DIFFRACTION100
2.7579-2.90330.18555670.157910776X-RAY DIFFRACTION100
2.9033-3.08520.18155700.161710822X-RAY DIFFRACTION100
3.0852-3.32330.16835660.148910757X-RAY DIFFRACTION99
3.3233-3.65760.15565660.144810747X-RAY DIFFRACTION99
3.6576-4.18660.13685700.126310838X-RAY DIFFRACTION100
4.1866-5.27360.14125720.121710858X-RAY DIFFRACTION100
5.2736-47.60950.1745740.154910905X-RAY DIFFRACTION99

+
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