[English] 日本語
Yorodumi
- PDB-8ayj: Crystal structure of D-amino acid aminotransferase from Aminobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ayj
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiens complexed with 3-aminooxypropionic acid
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / Transaminase / DAAT / aminotransferase / complex / oxyme / 3-aminooxypropionic acid / Aminobacterium colombiens
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity
Similarity search - Function
: / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
Chem-OCF / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Biochem.J. / Year: 2023
Title: In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Authors: Shilova, S.A. / Matyuta, I.O. / Khrenova, M.G. / Nikolaeva, A.Y. / Klyachko, N.L. / Minyaev, M.E. / Khomutov, A.R. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase class IV
B: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8479
Polymers61,9542
Non-polymers1,8937
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-23 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.573, 58.434, 96.722
Angle α, β, γ (deg.)90.000, 94.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 0 - 275 / Label seq-ID: 2 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Aminotransferase class IV


Mass: 30976.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacterium colombiense (bacteria) / Strain: DSM 12261 / ALA-1 / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5
#2: Chemical
ChemComp-OCF / 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid / PYRIDOXAMINE-5'-PHOSPHATE linked to 3-aminooxypropionic acid


Mass: 334.219 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H15N2O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.02 M Sodium/potassium phosphate,0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.74503 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74503 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.869
11-h,-k,l20.131
ReflectionResolution: 1.75→48.24 Å / Num. obs: 56226 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.109 / Rrim(I) all: 0.196 / Net I/σ(I): 4.3 / Num. measured all: 167509
Reflection shell

Diffraction-ID: 1 / % possible all: 95.4

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.75-1.782.91.124862029470.4250.7611.3630.7
9.1-48.242.80.02911974230.9990.020.03518.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AHR

8ahr


Resolution: 1.75→48.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2084 / WRfactor Rwork: 0.1741 / FOM work R set: 0.7596 / SU B: 4.219 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1373 / SU Rfree: 0.1299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 2774 4.9 %RANDOM
Rwork0.201 ---
obs0.2029 53435 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.06 Å2 / Biso mean: 14.988 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20.24 Å2
2---0.96 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.75→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 122 406 4813
Biso mean--14.3 21.93 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134623
X-RAY DIFFRACTIONr_bond_other_d0.0030.0154406
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.6526290
X-RAY DIFFRACTIONr_angle_other_deg1.4091.56610198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3865576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55821.62216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49115805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9951531
X-RAY DIFFRACTIONr_chiral_restr0.1010.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025095
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02965
Refine LS restraints NCS

Ens-ID: 1 / Number: 8865 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.751→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 197 -
Rwork0.324 3840 -
all-4037 -
obs--96.28 %

+
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