[English] 日本語
Yorodumi
- PDB-2qez: Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qez
TitleCrystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution
ComponentsEthanolamine ammonia-lyase heavy chain
KeywordsLYASE / YP_013784.1 / ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia lyase large subunit (EutB) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


lyase / ethanolamine ammonia-lyase heavy chain domain like / Ribosomal Protein L24e; Chain: T; / Annexin V; domain 1 / Aldolase class I / Roll / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Beta ...lyase / ethanolamine ammonia-lyase heavy chain domain like / Ribosomal Protein L24e; Chain: T; / Annexin V; domain 1 / Aldolase class I / Roll / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes serotype 4b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)304,65012
Polymers304,0976
Non-polymers5536
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Ethanolamine ammonia-lyase heavy chain
F: Ethanolamine ammonia-lyase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6425
Polymers101,3662
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-19 kcal/mol
Surface area31870 Å2
MethodPISA
3
D: Ethanolamine ammonia-lyase heavy chain
E: Ethanolamine ammonia-lyase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5504
Polymers101,3662
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area32190 Å2
MethodPISA
4
B: Ethanolamine ammonia-lyase heavy chain
C: Ethanolamine ammonia-lyase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4583
Polymers101,3662
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-14 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.330, 223.700, 65.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 453 / Label seq-ID: 2 - 454

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

-
Components

#1: Protein
Ethanolamine ammonia-lyase heavy chain /


Mass: 50682.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 4b (bacteria)
Strain: F2365 / Gene: YP_013784.1, eutB, LMOf2365_1185 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q720Q3, ethanolamine ammonia-lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 30.0% 2-methyl-2,4-pentanediol, 0.2M Magnesium acetate, 0.1M Sodium pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97925, 0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979251
30.978951
ReflectionResolution: 2.15→29.21 Å / Num. obs: 162506 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.807 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.170.4871.53948627770194.6
2.17-2.260.4491.84776032469199.2
2.26-2.360.3792.14725230639199.7
2.36-2.490.3032.75190832782199.8
2.49-2.640.2353.54952530299199.7
2.64-2.850.174.85432032306199.7
2.85-3.130.1067.65269030696199.6
3.13-3.590.05813.15487131788199.4
3.59-4.510.03235371230959199.4
4.51-29.210.01932.25440230960197.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.943 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.219
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 8067 5 %RANDOM
Rwork0.228 ---
obs0.23 161942 99.27 %-
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: 48.229 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2---1.03 Å20 Å2
3---3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19677 0 36 754 20467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02220159
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218134
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.95127320
X-RAY DIFFRACTIONr_angle_other_deg1.085341997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.40252631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24324.947857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.528153291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2711599
X-RAY DIFFRACTIONr_chiral_restr0.0630.23148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222831
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023930
X-RAY DIFFRACTIONr_nbd_refined0.2010.34799
X-RAY DIFFRACTIONr_nbd_other0.1610.319314
X-RAY DIFFRACTIONr_nbtor_refined0.1780.510288
X-RAY DIFFRACTIONr_nbtor_other0.090.511538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.51589
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.516
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.54
X-RAY DIFFRACTIONr_mcbond_it1.662313395
X-RAY DIFFRACTIONr_mcbond_other0.68535436
X-RAY DIFFRACTIONr_mcangle_it2.663520865
X-RAY DIFFRACTIONr_scbond_it4.91887627
X-RAY DIFFRACTIONr_scangle_it6.576116455
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2447MEDIUM POSITIONAL0.220.5
2B2447MEDIUM POSITIONAL0.180.5
3C2447MEDIUM POSITIONAL0.260.5
4D2447MEDIUM POSITIONAL0.190.5
5E2447MEDIUM POSITIONAL0.170.5
6F2447MEDIUM POSITIONAL0.240.5
1A3346LOOSE POSITIONAL0.45
2B3346LOOSE POSITIONAL0.465
3C3346LOOSE POSITIONAL0.575
4D3346LOOSE POSITIONAL0.445
5E3346LOOSE POSITIONAL0.435
6F3346LOOSE POSITIONAL0.445
1A2447MEDIUM THERMAL1.652
2B2447MEDIUM THERMAL1.132
3C2447MEDIUM THERMAL1.472
4D2447MEDIUM THERMAL1.092
5E2447MEDIUM THERMAL1.052
6F2447MEDIUM THERMAL1.112
1A3346LOOSE THERMAL4.5510
2B3346LOOSE THERMAL3.110
3C3346LOOSE THERMAL4.0910
4D3346LOOSE THERMAL310
5E3346LOOSE THERMAL3.0110
6F3346LOOSE THERMAL3.0910
LS refinement shellResolution: 2.15→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 549 -
Rwork0.395 10691 -
obs-11240 94.44 %

+
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