[English] 日本語
Yorodumi
- PDB-8i7u: Crystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i7u
TitleCrystal structure of alpha-Oxoamine Synthase Alb29 with PLP cofactor
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / complex / PLP / L-glutamate / Dimer / alpha-Oxoamine Synthase
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesStreptomyces albogriseolus 1-36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsXu, M.J. / Zhang, D.K.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)No. 2022YFC2804100 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and mechanistic investigations on CC bond forming alpha-oxoamine synthase allowing L-glutamate as substrate.
Authors: Zhang, D.K. / Song, K.Y. / Yan, Y.Q. / Zheng, J.T. / Xu, J. / Da, L.T. / Xu, M.J.
History
DepositionFeb 2, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 8-amino-7-oxononanoate synthase
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase
D: 8-amino-7-oxononanoate synthase
E: 8-amino-7-oxononanoate synthase
F: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,58212
Polymers255,0996
Non-polymers1,4836
Water3,027168
1
C: 8-amino-7-oxononanoate synthase
F: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5274
Polymers85,0332
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-32 kcal/mol
Surface area27340 Å2
MethodPISA
2
A: 8-amino-7-oxononanoate synthase
E: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5274
Polymers85,0332
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-36 kcal/mol
Surface area27470 Å2
MethodPISA
3
B: 8-amino-7-oxononanoate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)85,5274
Polymers85,0332
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area7780 Å2
ΔGint-37 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.465, 110.462, 353.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

-
Components

#1: Protein
8-amino-7-oxononanoate synthase / alpha-oxoamine synthases


Mass: 42516.488 Da / Num. of mol.: 6 / Mutation: S87G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus 1-36 (bacteria)
Gene: alb29 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6B9KSL0, 8-amino-7-oxononanoate synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion
Details: 0.03M MgCl2, 0.03M CaCl2, 0.1M MES-Imidazole, pH 6.5, 20% Glycerol, 10%(w/v)PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 89611 / % possible obs: 98.04 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.06 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08688 / Rpim(I) all: 0.03505 / Rrim(I) all: 0.09387 / Net I/σ(I): 14.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible allΧ2
2.49-2.585.50.6342.588730.890.9710.29210.700898.72
2.58-2.632.60.484750997.20.606
2.63-2.682.80.392763498.40.436
2.68-2.742.90.343756998.30.442
2.74-2.82.80.306763798.40.447
2.8-2.862.80.269753397.80.489
2.86-2.932.80.223765798.10.542
2.93-3.012.90.201757898.60.602
3.01-3.12.80.164761098.10.452
3.1-3.22.70.137765198.30.449
3.2-3.312.80.118762598.50.453
3.31-3.452.80.126763098.30.606
3.45-3.62.80.129764498.40.61
3.6-3.792.80.075764698.50.48
3.79-4.032.70.071760398.10.569
4.03-4.342.90.054755998.10.425
4.34-4.782.80.049758798.30.459
4.78-5.472.80.051766898.30.514
5.47-6.892.80.048760798.30.47
6.89-502.80.041765198.41.44

-
Processing

Software
NameVersionClassification
REFMAC7.1.018refinement
PHENIX1.19.2_4158refinement
HKL-2000data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→25.18 Å / SU ML: 0.3156 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 4536 5.07 %
Rwork0.1967 84921 -
obs0.1995 89457 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.05 Å2
Refinement stepCycle: LAST / Resolution: 2.49→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17740 0 90 168 17998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007618159
X-RAY DIFFRACTIONf_angle_d0.95224602
X-RAY DIFFRACTIONf_chiral_restr0.05442775
X-RAY DIFFRACTIONf_plane_restr0.0093195
X-RAY DIFFRACTIONf_dihedral_angle_d14.18476560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.34241660.2592810X-RAY DIFFRACTION96.88
2.52-2.550.33551380.25292782X-RAY DIFFRACTION99.86
2.55-2.580.26751720.24262791X-RAY DIFFRACTION99.53
2.58-2.610.33271600.23612854X-RAY DIFFRACTION99.8
2.61-2.650.30541480.23822807X-RAY DIFFRACTION99.63
2.65-2.680.32551360.24472866X-RAY DIFFRACTION99.77
2.68-2.720.34961490.24162864X-RAY DIFFRACTION99.83
2.72-2.760.32771350.2312849X-RAY DIFFRACTION99.93
2.76-2.80.34021510.22312807X-RAY DIFFRACTION99.9
2.8-2.850.29331670.21992901X-RAY DIFFRACTION99.87
2.85-2.90.28551430.21672805X-RAY DIFFRACTION99.9
2.9-2.950.25381570.20672851X-RAY DIFFRACTION99.93
2.95-3.010.33161630.21942813X-RAY DIFFRACTION99.57
3.01-3.070.30561540.22082870X-RAY DIFFRACTION99.74
3.07-3.140.3151900.21492824X-RAY DIFFRACTION99.93
3.14-3.210.29341610.22452815X-RAY DIFFRACTION99.87
3.21-3.290.30261530.22492891X-RAY DIFFRACTION99.84
3.29-3.380.2641470.21712840X-RAY DIFFRACTION99.9
3.38-3.480.24241260.21172890X-RAY DIFFRACTION99.67
3.48-3.590.28541450.20692877X-RAY DIFFRACTION99.9
3.59-3.720.2941950.20191747X-RAY DIFFRACTION60.87
3.72-3.870.23311480.19612887X-RAY DIFFRACTION99.77
3.87-4.040.25061470.18142884X-RAY DIFFRACTION99.74
4.04-4.250.23541390.1782912X-RAY DIFFRACTION99.87
4.25-4.520.16491370.16192901X-RAY DIFFRACTION99.8
4.52-4.860.21451570.16212892X-RAY DIFFRACTION99.48
4.86-5.350.22421620.18332950X-RAY DIFFRACTION99.68
5.35-6.110.25831530.19422945X-RAY DIFFRACTION99.61
6.11-7.670.21581600.19162948X-RAY DIFFRACTION99.3
7.67-25.180.18121770.15813048X-RAY DIFFRACTION97.58

+
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