[English] 日本語
Yorodumi
- PDB-8yrv: Crystal structure of D-amino acid transaminase from Haliscomenoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yrv
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / complex / transaminase / aminotransferase / D-amino acid / 3-aminooxypropionic acid / oxyme
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity / metal ion binding
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 / Aminotransferase class IV
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis DSM 1100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Nikolaeva, A.Y. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Naturae / Year: 2024
Title: Insights into the Functioning of the D-amino Acid Transaminase from Haliscomenobacter Hydrossis via a Structural and Spectral Analysis of its Complex with 3-Aminooxypropionic Acid.
Authors: Bakunova, A.K. / Matyuta, I.O. / Nikolaeva, A.Y. / Boyko, K.M. / Khomutov, A.R. / Bezsudnova, E.Y. / Popov, V.O.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6803
Polymers32,3221
Non-polymers3592
Water5,531307
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3616
Polymers64,6442
Non-polymers7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area4730 Å2
ΔGint-21 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.772, 71.232, 52.549
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Aminotransferase class IV


Mass: 32321.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis DSM 1100 (bacteria)
Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#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.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M Bis-tris pH 5.5, 25% PEG 3350, 6mM PLP, 12mM 3-aminooxypropionic acid

-
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 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74503 Å / Relative weight: 1
ReflectionResolution: 1.7→35.34 Å / Num. obs: 32789 / % possible obs: 94.9 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.054 / Rrim(I) all: 0.1 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 107399
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.484 / Num. measured all: 6072 / Num. unique obs: 1795 / CC1/2: 0.602 / Rpim(I) all: 0.312 / Rrim(I) all: 0.578 / Χ2: 0.52 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.8data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.51 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 1667 5.1 %RANDOM
Rwork0.16569 ---
obs0.16793 31120 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.28 Å2
2--0.2 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.7→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 23 307 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132352
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152239
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6493189
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5765125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38921.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0471522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
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_it1.441.5161126
X-RAY DIFFRACTIONr_mcbond_other1.4391.5141123
X-RAY DIFFRACTIONr_mcangle_it2.1282.2621405
X-RAY DIFFRACTIONr_mcangle_other2.1282.2621405
X-RAY DIFFRACTIONr_scbond_it2.151.7751226
X-RAY DIFFRACTIONr_scbond_other2.1291.7711221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3412.571780
X-RAY DIFFRACTIONr_long_range_B_refined4.96819.2082807
X-RAY DIFFRACTIONr_long_range_B_other4.77718.6852735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 133 -
Rwork0.257 2363 -
obs--98.58 %

+
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