[English] 日本語
Yorodumi
- PDB-7do6: Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7do6
TitleCrystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(NADP bound-form)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / L-Rhamnose metabolism / NADP-dependent dehydrogenase / SDR protein family
Function / homologyPKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsYoshiwara, K. / Watanabe, Y. / Watanabe, S.
CitationJournal: Febs Lett. / Year: 2021
Title: Crystal structure of l-rhamnose 1-dehydrogenase involved in the nonphosphorylative pathway of l-rhamnose metabolism in bacteria.
Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y.
History
DepositionDec 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,71216
Polymers221,7658
Non-polymers5,9478
Water6,918384
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8568
Polymers110,8834
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-125 kcal/mol
Surface area31280 Å2
MethodPISA
2
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8568
Polymers110,8834
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-120 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.633, 81.571, 86.389
Angle α, β, γ (deg.)87.680, 75.530, 89.350
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Short-chain dehydrogenase/reductase SDR / L-Rhamnose 1-dehydrogenase


Mass: 27720.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / Gene: Avin_09160 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: C1DMX5
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-Rhamnose 1-dehydrogenase / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M NaCl, 24.5% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50.03 Å / Num. obs: 82779 / % possible obs: 96.1 % / Redundancy: 2.185 % / Biso Wilson estimate: 40.602 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.268 / Χ2: 0.729 / Net I/σ(I): 3.68 / Num. measured all: 354663
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.37-2.512.1491.0030.925443927248253330.4331.31193
2.51-2.692.10.691.35171525640246240.6060.90596
2.69-2.92.1580.5041.825034823938233300.7390.66197.5
2.9-3.182.2890.3632.74903921926214270.8260.47697.7
3.18-3.552.2390.2274.174324319920193110.9130.29996.9
3.55-4.12.1140.1525.633570017488168840.9540.296.5
4.1-5.012.2430.1037.953187714808142090.9740.13596
5.01-7.052.1970.117.492434211482110790.970.14496.5
7.05-50.032.2830.07111.513960644461160.9820.09294.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→50.03 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.37 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2573 4170 5.04 %
Rwork0.2049 78609 -
obs0.2076 82779 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.34 Å2 / Biso mean: 33.795 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 2.37→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13988 0 384 384 14756
Biso mean--48.6 33.66 -
Num. residues----1994
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.37-2.39660.35991280.3142223384
2.3966-2.42480.41541490.3006256998
2.4248-2.45440.35171350.3007266198
2.4544-2.48540.35691310.3027258598
2.4854-2.51810.34711190.2913264398
2.5181-2.55260.3411310.2733266698
2.5526-2.58910.33561290.2719261898
2.5891-2.62780.3581400.2729265498
2.6278-2.66880.32631560.2603257698
2.6688-2.71260.33081270.2586268099
2.7126-2.75930.32481300.2422258698
2.7593-2.80950.32061270.2453270999
2.8095-2.86350.25491310.2278257899
2.8635-2.9220.29941420.2232266499
2.922-2.98550.29521320.2224265199
2.9855-3.05490.27891380.2112262699
3.0549-3.13130.27231390.2104267399
3.1313-3.2160.25961530.208259399
3.216-3.31060.2491630.1944262099
3.3106-3.41740.27541510.1944265899
3.4174-3.53950.23031300.1838264999
3.5395-3.68120.22791460.1811259999
3.6812-3.84870.23561420.1758265099
3.8487-4.05150.20071290.1702267099
4.0515-4.30520.19451540.1576264099
4.3052-4.63740.19771510.146259899
4.6374-5.10370.19391250.1605267699
5.1037-5.84120.24581330.1948265399
5.8412-7.35560.24891500.2018263099
7.3556-50.030.20641590.1783260198

+
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