[English] 日本語
Yorodumi
- PDB-4koa: Crystal Structure Analysis of 1,5-anhydro-D-fructose reductase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4koa
TitleCrystal Structure Analysis of 1,5-anhydro-D-fructose reductase from Sinorhizobium meliloti
Components1,5-anhydro-D-fructose reductase
KeywordsOXIDOREDUCTASE / GFO/IDH/MOCA family / Dehydrogenase / Sugar binding
Function / homology
Function and homology information


1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming) / 1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming) activity
Similarity search - Function
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 ...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
Chem-NDP / 1,5-anhydro-D-fructose reductase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSchu, M. / Faust, A. / Stosik, B. / Kohring, G.-W. / Giffhorn, F. / Scheidig, A.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The structure of substrate-free 1,5-anhydro-D-fructose reductase from Sinorhizobium meliloti 1021 reveals an open enzyme conformation.
Authors: Schu, M. / Faust, A. / Stosik, B. / Kohring, G.W. / Giffhorn, F. / Scheidig, A.J.
History
DepositionMay 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 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: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6392
Polymers34,8931
Non-polymers7451
Water5,116284
1
A: 1,5-anhydro-D-fructose reductase
hetero molecules

A: 1,5-anhydro-D-fructose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2784
Polymers69,7872
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5470 Å2
ΔGint-24 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.895, 89.672, 94.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

-
Components

#1: Protein 1,5-anhydro-D-fructose reductase / / Anhydrofructose reductase / 1 / 5-anhydro-D-fructose reductase (1 / 5-anhydro-D-mannitol-forming)


Mass: 34893.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: afr, R03305, SMc04400 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q92KZ3, 1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM BisTRIS, 50 mM ammonium sulphate, 20 % (w/v) PEG-3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 16, 2008 / Details: Incoatec mirror
RadiationMonochromator: Incoatec mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→19.5 Å / Num. all: 22202 / Num. obs: 22202 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 24.574 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 26.85
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.66 / Num. unique all: 1487 / Rsym value: 0.58 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GLX

2glx


Resolution: 1.93→19.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.103 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20971 1111 5 %RANDOM
Rwork0.15801 ---
all0.16061 22202 --
obs0.16061 21091 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---1.08 Å20 Å2
3---0.15 Å2
Refine analyzeLuzzati coordinate error free: 0.152 Å
Refinement stepCycle: LAST / Resolution: 1.93→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 48 284 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192622
X-RAY DIFFRACTIONr_bond_other_d0.0020.022489
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9673582
X-RAY DIFFRACTIONr_angle_other_deg0.96335703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1465350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.323.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.171522
X-RAY DIFFRACTIONr_chiral_restr0.1340.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 79 -
Rwork0.186 1496 -
obs--98.31 %

+
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