[English] 日本語
Yorodumi
- PDB-2g6w: Suicide inhibition of a-Oxamine Synthase: Structures of the Coval... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g6w
TitleSuicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of 8-Amino-7-oxonanoate Synthase with trifluoroalanine
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / biotin / 8-amino-7-oxonanoate / synthase / PLP / fluoroalanine
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LLF / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsAlexeev, D.
CitationJournal: Org.Biomol.Chem. / Year: 2006
Title: Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine.
Authors: Alexeev, D. / Baxter, R.L. / Campopiano, D.J. / Kerbarh, O. / Sawyer, L. / Tomczyk, N. / Watt, R. / Webster, S.P.
History
DepositionFeb 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9512
Polymers41,6411
Non-polymers3101
Water3,657203
1
A: 8-amino-7-oxononanoate synthase
hetero molecules

A: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9034
Polymers83,2822
Non-polymers6202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area9630 Å2
ΔGint-45 kcal/mol
Surface area26680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.670, 58.670, 198.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsThe second part of the biological assembly is generated by the crystallographic two fold axis

-
Components

#1: Protein 8-amino-7-oxononanoate synthase / AONS / 8-amino-7-ketopelargonate synthase / 7-keto-8-amino-pelargonic acid synthetase / 7-KAP ...AONS / 8-amino-7-ketopelargonate synthase / 7-keto-8-amino-pelargonic acid synthetase / 7-KAP synthetase / L-alanine-pimelyl CoA ligase


Mass: 41641.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P12998, 8-amino-7-oxononanoate synthase
#2: Chemical ChemComp-LLF / (4-{(E)-[(2,2-DIFLUOROETHYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / (E)-N-(2,2-DIFLUOROETHYL)PYRIDOXIMINE-5'-PHOSPHATE


Mass: 310.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13F2N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.2M AMMONIUM SULPHATE, 200MM BIS-TRIS, pH 7.0, EVAPORATION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 32000 / Num. obs: 22100 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→1.93 Å / % possible all: 99

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
PDB_EXTRACT1.701data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→21.41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.274 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24642 689 3.2 %RANDOM
Rwork0.17627 ---
obs0.17856 20556 96.17 %-
all-20559 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å20 Å2
2---0.31 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.14→21.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 20 203 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9584070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5223.212137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36415479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4751528
X-RAY DIFFRACTIONr_chiral_restr0.1550.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.31422
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.52029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.391
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.94321952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.87733011
X-RAY DIFFRACTIONr_scbond_it2.13121194
X-RAY DIFFRACTIONr_scangle_it3.03931059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.141→2.197 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 53 -
Rwork0.198 1450 -
obs--92.61 %
Refinement TLS params.Method: refined / Origin x: 5.6819 Å / Origin y: -1.9936 Å / Origin z: 46.4329 Å
111213212223313233
T0.1183 Å2-0.0035 Å2-0.0705 Å2-0.0012 Å2-0.004 Å2--0.075 Å2
L0.3647 °2-0.4844 °20.2968 °2-0.6415 °20.0664 °2--0.9263 °2
S-0.094 Å °-0.0106 Å °0.1787 Å °-0.0008 Å °0.0324 Å °-0.1153 Å °-0.182 Å °0.0799 Å °0.0617 Å °

+
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