[English] 日本語
Yorodumi
- PDB-7xrn: Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presenc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xrn
TitleEthanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate
Components(Ethanolamine ammonia-lyase ...) x 2
KeywordsLYASE / Adenosylcobalamin / Radical enzyme
Function / homology
Function and homology information


ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol
Similarity search - Function
Ethanolamine ammonia-lyase small subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase light chain, C-terminal / Ethanolamine ammonia-lyase heavy chain, domain 2 / Ethanolamine ammonia-lyase heavy chain, N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / Ethanolamine ammonia lyase large subunit (EutB) / Aldolase-type TIM barrel
Similarity search - Domain/homology
COBALAMIN / Chem-FWK / AMMONIUM ION / Ethanolamine ammonia-lyase large subunit / Ethanolamine ammonia-lyase small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsShibata, N. / Toraya, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemistry / Year: 2022
Title: Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Authors: Shibata, N. / Higuchi, Y. / Krautler, B. / Toraya, T.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,21416
Polymers156,4344
Non-polymers3,78012
Water13,854769
1
A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules

A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules

A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,64148
Polymers469,30112
Non-polymers11,34036
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area63620 Å2
ΔGint-189 kcal/mol
Surface area121860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.383, 242.383, 76.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

-
Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD

#1: Protein Ethanolamine ammonia-lyase large subunit / EAL large subunit / Ethanolamine ammonia-lyase alpha subunit / Ethanolamine ammonia-lyase heavy ...EAL large subunit / Ethanolamine ammonia-lyase alpha subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine deaminase large subunit


Mass: 49447.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutB, b2441, JW2434 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase
#2: Protein Ethanolamine ammonia-lyase small subunit / EAL small subunit / Ethanolamine ammonia-lyase beta subunit / Ethanolamine ammonia-lyase light ...EAL small subunit / Ethanolamine ammonia-lyase beta subunit / Ethanolamine ammonia-lyase light chain / Ethanolamine deaminase small subunit


Mass: 28769.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutC, b2440, JW2433 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P19636, ethanolamine ammonia-lyase

-
Non-polymers , 5 types, 781 molecules

#3: Chemical ChemComp-FWK / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol


Mass: 265.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (w/v) PEG 6000, 0.1 M Ammonium chloride, and 0.05 M HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→49 Å / Num. obs: 156031 / % possible obs: 99.9 % / Redundancy: 6.82 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.77
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 156031 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABR

3abr


Resolution: 2.07→48.16 Å / Cross valid method: FREE R-VALUE / σ(F): 60.09 / Phase error: 29.243
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.241 7806 5.01 %
Rwork0.214 --
obs0.216 156031 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.85 Å2
Refinement stepCycle: LAST / Resolution: 2.07→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 256 769 11785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211253
X-RAY DIFFRACTIONf_angle_d0.85615321
X-RAY DIFFRACTIONf_dihedral_angle_d9.8111685
X-RAY DIFFRACTIONf_chiral_restr0.0441757
X-RAY DIFFRACTIONf_plane_restr0.0041997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.3223700.27297217X-RAY DIFFRACTION94
2.11-2.150.31623490.26977417X-RAY DIFFRACTION95
2.15-2.190.30114010.26067353X-RAY DIFFRACTION95
2.19-2.230.27743940.25647359X-RAY DIFFRACTION95
2.23-2.280.28613750.24697383X-RAY DIFFRACTION95
2.28-2.330.28553930.2487414X-RAY DIFFRACTION95
2.33-2.390.27383650.24337399X-RAY DIFFRACTION95
2.39-2.460.25223810.2367371X-RAY DIFFRACTION95
2.46-2.530.24024030.22957374X-RAY DIFFRACTION95
2.53-2.610.24453750.22677412X-RAY DIFFRACTION95
2.61-2.70.25793960.22317407X-RAY DIFFRACTION95
2.7-2.810.24674000.21967400X-RAY DIFFRACTION95
2.81-2.940.24343860.21717400X-RAY DIFFRACTION95
2.94-3.090.24834050.2137407X-RAY DIFFRACTION95
3.09-3.290.22544040.20757408X-RAY DIFFRACTION95
3.29-3.540.22873920.20017421X-RAY DIFFRACTION95
3.54-3.90.21193770.19427453X-RAY DIFFRACTION95
3.9-4.460.20344180.18017467X-RAY DIFFRACTION95
4.46-5.620.21273860.19087519X-RAY DIFFRACTION95
5.62-48.160.25964360.2267644X-RAY DIFFRACTION95
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)
10.8657-0.2251-0.02830.7030.00860.34060.05880.131-0.3466-0.0826-0.03320.04370.06950.0303-0.01720.25130.0139-0.03290.134-0.06290.3019-113.675133.6351-5.8516
20.2098-0.162-0.05680.26630.03820.01790.05880.3372-0.414-0.2746-0.06550.05340.1044-0.08370.06770.53370.0551-0.09290.2968-0.35050.655-118.811513.774-24.6943
30.9913-0.1116-0.04170.76520.0320.45310.05480.0712-0.404-0.0686-0.00540.23740.0605-0.1429-0.01970.19340.0004-0.05930.1698-0.01520.3419-148.141244.3589-0.2459
40.77190.5508-0.17220.5392-0.16510.2179-0.0038-0.2705-0.47430.13570.04310.31940.1929-0.1796-0.03760.3918-0.06140.03750.3440.21010.8264-155.340124.978218.4585
51.39660.0162-0.60073.15540.37022.8698-0.05910.3008-0.4951-0.27720.0596-0.06950.4207-0.04040.00140.39930.0242-0.0460.2559-0.14760.4593-112.641321.3618-15.798
61.2089-0.89020.07960.68090.16912.0767-0.044-0.0243-0.1198-0.0489-0.05590.06320.02250.03080.08210.3203-0.0418-0.01060.32030.13510.6211-156.437134.058210.0038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 1 THROUGH 453)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 44 THROUGH 295)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 1 THROUGH 453)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 44 THROUGH 295)
5X-RAY DIFFRACTION5(CHAIN 'B' AND RESID 601)
6X-RAY DIFFRACTION6(CHAIN 'D' AND RESID 601)

+
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