[English] 日本語
Yorodumi
- PDB-4ya6: Crystal structure of LigO-apo form from Sphingobium sp. strain SYK-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ya6
TitleCrystal structure of LigO-apo form from Sphingobium sp. strain SYK-6
ComponentsC alpha-dehydrogenase
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase/reductase SDR family
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
C alpha-dehydrogenase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.799 Å
AuthorsPereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Authors: Pereira, J.H. / Heins, R.A. / Gall, D.L. / McAndrew, R.P. / Deng, K. / Holland, K.C. / Donohue, T.J. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Adams, P.D.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C alpha-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)32,7611
Polymers32,7611
Non-polymers00
Water2,558142
1
A: C alpha-dehydrogenase

A: C alpha-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)65,5222
Polymers65,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6290 Å2
ΔGint-55 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.229, 79.229, 72.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein C alpha-dehydrogenase / Calpha-dehydrogenase


Mass: 32761.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligO, SLG_35880 / Production host: Escherichia coli (E. coli) / References: UniProt: C0SUK3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium Citrate, 0.1 M MES pH 5.5, 20% PEG 3,350, 5% Isopropanol
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 24752 / % possible obs: 100 % / Redundancy: 10.8 % / Net I/σ(I): 46.3

-
Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.799→50 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 1934 8.14 %
Rwork0.1777 --
obs0.18 23770 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 0 142 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032115
X-RAY DIFFRACTIONf_angle_d0.7732861
X-RAY DIFFRACTIONf_dihedral_angle_d14.094781
X-RAY DIFFRACTIONf_chiral_restr0.029315
X-RAY DIFFRACTIONf_plane_restr0.003378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7992-1.84420.30951210.25171373X-RAY DIFFRACTION85
1.8442-1.8940.29141230.2291419X-RAY DIFFRACTION89
1.894-1.94980.25921330.20681451X-RAY DIFFRACTION91
1.9498-2.01270.22391310.20511512X-RAY DIFFRACTION94
2.0127-2.08460.24641360.1981556X-RAY DIFFRACTION97
2.0846-2.16810.23371420.18561546X-RAY DIFFRACTION98
2.1681-2.26680.23841420.19881582X-RAY DIFFRACTION98
2.2668-2.38630.22511370.18071589X-RAY DIFFRACTION98
2.3863-2.53580.23521400.19271576X-RAY DIFFRACTION98
2.5358-2.73160.24811410.18191601X-RAY DIFFRACTION98
2.7316-3.00640.20011440.19211606X-RAY DIFFRACTION99
3.0064-3.44140.17141460.17091650X-RAY DIFFRACTION100
3.4414-4.33540.17551480.151647X-RAY DIFFRACTION100
4.3354-49.75110.19741500.1711728X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2757-0.1401-0.93921.2740.31392.6629-0.0591-0.4988-0.03680.18370.05070.1177-0.1882-0.3471-0.01660.23290.06820.01020.37790.01690.17467.407536.790722.5982
21.1072-0.4056-0.25051.10890.30633.9864-0.0732-0.1396-0.05850.00230.01010.0827-0.4523-0.34020.05790.15130.03820.00840.21910.01220.24568.623333.47816.9689
31.2064-0.1051-0.33291.00470.46952.41460.0245-0.1856-0.18990.02910.01080.09780.0257-0.07340.0020.19240.01970.00560.24610.02610.29113.250527.51947.4412
44.4146-1.01531.54021.1483-0.25133.1519-0.0302-0.1331-0.2810.09110.02510.30250.2237-0.54630.15170.2213-0.04120.01620.31820.06930.39781.25222.50158.8532
51.3781-0.9416-0.42082.06832.24544.8024-0.0095-0.0939-0.59030.0277-0.130.32750.374-0.53830.11870.3004-0.1150.03950.3440.05610.52892.2914.98716.968
65.5629-1.91431.28956.1751-2.35586.44950.4857-0.4317-0.284-0.50340.04940.59380.62980.59070.19350.71970.00540.21930.5601-0.1680.947324.2541-5.9648-5.6452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 273 )
6X-RAY DIFFRACTION6chain 'A' and (resid 274 through 295 )

+
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