[English] 日本語
Yorodumi
- PDB-6p5u: Structure of an enoyl-CoA hydratase/aldolase isolated from a lign... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p5u
TitleStructure of an enoyl-CoA hydratase/aldolase isolated from a lignin-degrading consortium
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / lignin / ferulic acid / vanillin / enoyl-CoA hydratase/aldolase
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLiberato, M.V. / Squina, F.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/50590-4 Brazil
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: The structure of a prokaryotic feruloyl-CoA hydratase-lyase from a lignin-degrading consortium with high oligomerization stability under extreme pHs.
Authors: Liberato, M.V. / Araujo, J.N. / Sodre, V. / Goncalves, T.A. / Vilela, N. / Moraes, E.C. / Garcia, W. / Squina, F.M.
History
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
D: Enoyl-CoA hydratase
E: Enoyl-CoA hydratase
F: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,80613
Polymers187,9186
Non-polymers4,8887
Water21,4561191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24970 Å2
ΔGint-123 kcal/mol
Surface area49000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.280, 130.960, 115.910
Angle α, β, γ (deg.)90.000, 90.680, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Enoyl-CoA hydratase


Mass: 31319.721 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Gene: Ech / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1BT02
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1191 / 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: 38.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 25% PEG3000, 0.1 M Tri-sodium citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.1→46.96 Å / Num. obs: 85256 / % possible obs: 98.9 % / Redundancy: 2.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.091 / Rrim(I) all: 0.156 / Net I/σ(I): 7.1 / Num. measured all: 235067 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.142.70.6841205945490.5530.5040.8541.699.6
11.11-46.962.80.04714845380.9680.0380.06130.588.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.92 Å46.96 Å
Translation6.92 Å46.96 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J5I

2j5i


Resolution: 2.1→43.398 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2285 4212 4.94 %
Rwork0.196 --
obs0.1976 85218 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.78 Å2 / Biso mean: 25.2935 Å2 / Biso min: 3.3 Å2
Refinement stepCycle: final / Resolution: 2.1→43.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11012 0 307 1191 12510
Biso mean--31.34 34.62 -
Num. residues----1446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.33881510.273627102861100
2.1239-2.14880.31751400.26327072847100
2.1488-2.17510.31241510.260126872838100
2.1751-2.20260.2961550.256527292884100
2.2026-2.23160.29091380.246227092847100
2.2316-2.26210.28661270.2427612888100
2.2621-2.29440.29581330.22927192852100
2.2944-2.32870.27481300.22927252855100
2.3287-2.36510.29361210.22812704282599
2.3651-2.40390.26391550.21172645280098
2.4039-2.44530.26571240.2182691281599
2.4453-2.48980.25621530.20722734288799
2.4898-2.53760.23811380.210726902828100
2.5376-2.58940.30781320.2127222854100
2.5894-2.64570.2441330.203427352868100
2.6457-2.70730.23411610.197926792840100
2.7073-2.7750.24161360.194927532889100
2.775-2.850.20651230.197627582881100
2.85-2.93380.22821290.186127252854100
2.9338-3.02850.22181600.1852676283699
3.0285-3.13670.23231670.19412681284899
3.1367-3.26230.18881350.17922667280298
3.2623-3.41070.21321420.17572690283297
3.4107-3.59040.21061260.16652671279798
3.5904-3.81520.1711600.15912703286399
3.8152-4.10960.1891360.15462734287099
4.1096-4.52280.16351450.14262679282498
4.5228-5.17630.17351470.16572661280897
5.1763-6.51810.23261410.21772640278196
6.5181-43.40710.23961230.2232621274493
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)
10.4073-0.0377-0.12570.6439-0.09241.07880.0235-0.00770.0983-0.0614-0.0063-0.0214-0.15890.0401-0.0240.2062-0.0102-0.01060.1514-0.00070.194418.68-6.200512.7611
20.7222-0.08210.14430.726-0.02820.58910.0137-0.07350.01350.0424-0.00880.0552-0.0114-0.1036-0.00420.1798-0.0107-0.00710.19890.00060.17780.4965-28.028328.9111
30.96810.40390.09430.6533-0.04510.6044-0.01540.1059-0.1158-0.04230.0267-0.06470.13310.04460.00090.20380.02530.0020.146-0.01860.161523.804-38.41388.1792
40.75810.2457-0.04430.71180.00020.59780.04670.0276-0.0797-0.0001-0.0215-0.12630.0560.1625-0.01620.18840.0262-0.02460.2217-0.0070.198646.2277-38.003632.2588
50.6067-0.1239-0.10980.59720.26140.96470.0432-0.09580.0924-0.0030.012-0.06-0.25350.1938-0.0580.2215-0.07140.00070.2044-0.00310.177639.5497-5.207337.661
60.3639-0.14160.120.92070.02620.7236-0.0014-0.1041-0.00880.07280.02150.01220.044-0.0434-0.01610.2074-0.00510.00070.240.01470.192122.4062-28.8353.623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 12 through 254)A12 - 254
2X-RAY DIFFRACTION2(chain 'B' and resid 14 through 253)B14 - 253
3X-RAY DIFFRACTION3(chain 'C' and resid 12 through 253)C12 - 253
4X-RAY DIFFRACTION4(chain 'D' and resid 10 through 254)D10 - 254
5X-RAY DIFFRACTION5(chain 'E' and resid 9 through 254)E9 - 254
6X-RAY DIFFRACTION6(chain 'F' and resid 10 through 254)F10 - 254

+
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://pdbjlvh1.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