[English] 日本語
Yorodumi
- PDB-3afm: Crystal structure of aldose reductase A1-R responsible for algina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3afm
TitleCrystal structure of aldose reductase A1-R responsible for alginate metabolism
ComponentsCarbonyl reductase
KeywordsOXIDOREDUCTASE / ALPHA/BETA/ALPHA / ROSSMANN-FOLD
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTakase, R. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1
Authors: Takase, R. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionMar 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonyl reductase
B: Carbonyl reductase


Theoretical massNumber of molelcules
Total (without water)53,9612
Polymers53,9612
Non-polymers00
Water10,088560
1
A: Carbonyl reductase
B: Carbonyl reductase

A: Carbonyl reductase
B: Carbonyl reductase


Theoretical massNumber of molelcules
Total (without water)107,9224
Polymers107,9224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area11480 Å2
ΔGint-79 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.215, 106.215, 70.449
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1191-

HOH

-
Components

#1: Protein Carbonyl reductase / A1-R / 4-deoxy-L-erythro-5-hexoseulose-uronic acid reductase


Mass: 26980.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: A1 / Gene: a1-R / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6RU56, EC: 1.1.1.126
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 85mM tris-hydrochloride, 170mM lithium sulphate, 25.5% PEG 4000, 15% glycerol, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 19, 2008
RadiationMonochromator: Si(111) double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 55401 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 4.99 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPX

1spx


Resolution: 1.65→31.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.721 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20447 2807 5.1 %RANDOM
Rwork0.17603 ---
obs0.17746 52496 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 560 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213854
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9385234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0035526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82923.562160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79615599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5691523
X-RAY DIFFRACTIONr_chiral_restr0.0390.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023006
X-RAY DIFFRACTIONr_nbd_refined0.1880.21944
X-RAY DIFFRACTIONr_nbtor_refined0.30.22714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0860.2447
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.262
X-RAY DIFFRACTIONr_mcbond_it0.4751.52594
X-RAY DIFFRACTIONr_mcangle_it0.79724015
X-RAY DIFFRACTIONr_scbond_it1.25131404
X-RAY DIFFRACTIONr_scangle_it1.9794.51219
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 230 -
Rwork0.253 3796 -
obs--99.65 %

+
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