[English] 日本語
Yorodumi
- PDB-1yo6: Crystal Structure of the putative Carbonyl Reductase Sniffer of C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yo6
TitleCrystal Structure of the putative Carbonyl Reductase Sniffer of Caenorhabditis elegans
ComponentsPutative Carbonyl Reductase Sniffer
KeywordsOXIDOREDUCTASE / Tyrosine-dependent oxidoreductase (SDR family) / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SKN-1 Dependent Zygotic transcript
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSoutheast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of the putative Carbonyl Reductase Sniffer of Caenorhabditis elegans
Authors: Schormann, N. / Lu, S. / Symersky, J. / Karpova, E. / Zhang, Y. / Luo, D. / Zhou, Q. / Huang, W. / Luan, C.-H. / Gray, R. / Arabshahi, A. / McKinstry, A. / Qiu, S. / Cao, Z. / An, J. / Li, S. ...Authors: Schormann, N. / Lu, S. / Symersky, J. / Karpova, E. / Zhang, Y. / Luo, D. / Zhou, Q. / Huang, W. / Luan, C.-H. / Gray, R. / Arabshahi, A. / McKinstry, A. / Qiu, S. / Cao, Z. / An, J. / Li, S. / Lin, G. / Tsao, J. / Johnson, D. / Luo, M. / Shang, Q. / Chen, Y. / Stinnett, M. / Bunzel, R. / Carson, M. / Bray, T. / DeLucas, L.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: Putative Carbonyl Reductase Sniffer
B: Putative Carbonyl Reductase Sniffer
C: Putative Carbonyl Reductase Sniffer
D: Putative Carbonyl Reductase Sniffer
E: Putative Carbonyl Reductase Sniffer
F: Putative Carbonyl Reductase Sniffer


Theoretical massNumber of molelcules
Total (without water)160,3836
Polymers160,3836
Non-polymers00
Water4,252236
1
A: Putative Carbonyl Reductase Sniffer
B: Putative Carbonyl Reductase Sniffer


Theoretical massNumber of molelcules
Total (without water)53,4612
Polymers53,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-22 kcal/mol
Surface area18900 Å2
MethodPISA
2
C: Putative Carbonyl Reductase Sniffer
D: Putative Carbonyl Reductase Sniffer


Theoretical massNumber of molelcules
Total (without water)53,4612
Polymers53,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-24 kcal/mol
Surface area18970 Å2
MethodPISA
3
E: Putative Carbonyl Reductase Sniffer
F: Putative Carbonyl Reductase Sniffer


Theoretical massNumber of molelcules
Total (without water)53,4612
Polymers53,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-25 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.870, 86.320, 242.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a dimer (chains A,B; chains C,D; chains E,F). The asymmetric unit contains 3 independent homodimers.

-
Components

#1: Protein
Putative Carbonyl Reductase Sniffer / sniffer like family member (5L996)


Mass: 26730.551 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Apo-Enzyme / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Sniffer / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: P90780
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG2000 MME, 0.1M Tris, 0.1% beta-OG, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 46212 / Num. obs: 46212 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4124 / Rsym value: 0.205 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model was created by the SWISS-MODEL server based on PDB entry 1SNY using the C. elegans target sequence (C55A6.5)

1sny


Resolution: 2.6→47.12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6442715.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The following residues are not visible in the electron density: 205-217 chain A; 204-218 chain B; 208-217 chain C; 205-218 chain D; 1,204-217 chain E; 1,48-49,81-82,136-137,206-218 chain F
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2291 5 %RANDOM
Rwork0.218 ---
all0.219 45906 --
obs0.2181 45906 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5276 Å2 / ksol: 0.336883 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2---1.25 Å20 Å2
3---3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 0 236 10878
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 309 4.7 %
Rwork0.275 6334 -
obs-6643 82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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