[English] 日本語
Yorodumi
- PDB-3ao0: Crystal structure of ethanolamine ammonia-lyase from Escherichia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ao0
TitleCrystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-CBL and (S)-2-amino-1-propanol
Components(Ethanolamine ammonia-lyase ...) x 2
KeywordsLYASE / (BETA/ALPHA)8 FOLD / COBALT / COBALAMIN / Tim Barrel
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 light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / 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 light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / 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) / DNA Binding (I), subunit A / Ribosomal Protein L24e; Chain: T; / Annexin V; domain 1 / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminopropan-1-ol / COBALAMIN / 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: 2.25 Å
AuthorsShibata, N.
CitationJournal: Biochemistry / Year: 2011
Title: How coenzyme B12-dependent ethanolamine ammonia-lyase deals with both enantiomers of 2-amino-1-propanol as substrates: structure-based rationalization.
Authors: Shibata, N. / Higuchi, Y. / Toraya, T.
History
DepositionSep 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Non-polymer description
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2689
Polymers156,4344
Non-polymers2,8345
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14770 Å2
ΔGint-56 kcal/mol
Surface area45100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.850, 243.850, 76.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
/ NCS ensembles :
ID
1
2

-
Components

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

#1: Protein Ethanolamine ammonia-lyase heavy chain / / Ethanolamine ammonia-lyase 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 / Plasmid: PUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase
#2: Protein Ethanolamine ammonia-lyase light chain / / Ethanolamine ammonia-lyase small subunit


Mass: 28769.021 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 44-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutC, b2440, JW2433 / Plasmid: PUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase

-
Non-polymers , 4 types, 597 molecules

#3: Chemical ChemComp-2A1 / (2S)-2-aminopropan-1-ol


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#4: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 6.0-7.0% (W/V) PEG 4000, 24-26 % (V/V) GLYCEROL, 1.0 % (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD),0.1M IMIDAZOLE-HCL, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.93
DetectorType: BRUCKER DIP-6040 / Detector: IMAGE PLATE / Date: Jul 1, 2008 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.25→48 Å / Num. all: 121794 / Num. obs: 121794 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.3
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.95 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
BSSdata collection
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3ABR

3abr


Resolution: 2.25→48 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.779 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.257 6112 5 %RANDOM
Rwork0.235 ---
all0.236 115669 --
obs0.236 115669 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 193 592 11545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211138
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.831.99115148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.66651408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21524.374487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.936151881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6991584
X-RAY DIFFRACTIONr_chiral_restr0.220.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6991.56989
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.198211236
X-RAY DIFFRACTIONr_scbond_it2.34934149
X-RAY DIFFRACTIONr_scangle_it3.5114.53911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1779tight positional0.050.05
11C1611medium positional0.270.5
22B1118medium positional0.350.5
22D685loose positional0.35
11A1779tight thermal0.220.5
11C1611medium thermal0.292
22B1118medium thermal3.352
22D685loose thermal4.0510
LS refinement shellResolution: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 405 -
Rwork0.327 7993 -
obs--92.62 %
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)
10.3947-0.1658-0.0691.4416-0.02410.29980.04960.0399-0.0927-0.21550.00270.39350.04470.0397-0.05230.0809-0.0415-0.08860.1014-0.00880.173394.264-95.245-8.587
22.24960.1924-0.44822.09620.44240.70130.12930.3441-0.1702-0.9669-0.27111.3234-0.1511-0.14490.14180.53820.1048-0.71440.2255-0.21941.002174.2655-100.7676-27.313
30.4069-0.23170.07891.6479-0.07030.44730.02040.0177-0.03720.00410.01120.5163-0.0527-0.0028-0.03160.0635-0.0153-0.00370.0910.02680.213586.096-60.06-2.815
41.44240.5391-0.01092.98930.2371.33150.1355-0.1131-0.13650.98110.13931.8177-0.0574-0.2582-0.27480.39130.06260.72750.17150.21241.504565.424-63.83615.606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 453
2X-RAY DIFFRACTION2B44 - 295
3X-RAY DIFFRACTION3C1 - 453
4X-RAY DIFFRACTION4D44 - 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