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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yru
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / apo form / transaminase / aminotransferase / D-amino acid
Function / homology
Function and homology information


carboxylic acid biosynthetic process / branched-chain-amino-acid transaminase / 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
ACETATE ION / Chem-ZXN / branched-chain-amino-acid transaminase
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis DSM 1100 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Minyaev, M.E. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2024
Title: Incorporation of pyridoxal-5'-phosphate into the apoenzyme: A structural study of D-amino acid transaminase from Haliscomenobacter hydrossis.
Authors: Bakunova, A.K. / Matyuta, I.O. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _citation_author.name / _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)32,7183
Polymers32,3221
Non-polymers3962
Water2,234124
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4366
Polymers64,6442
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3590 Å2
ΔGint-19 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 71.780, 52.241
Angle α, β, γ (deg.)90.00, 100.72, 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZXN / [6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate


Mass: 337.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N3O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 45% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→21.43 Å / Num. obs: 21346 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.092 / Χ2: 0.95 / Net I/σ(I): 16.8 / Num. measured all: 119567
Reflection shellResolution: 2→2.05 Å / % possible obs: 89.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Num. measured all: 6358 / Num. unique obs: 1390 / CC1/2: 0.824 / Rpim(I) all: 0.276 / Rrim(I) all: 0.615 / Χ2: 0.91 / Net I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.08 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23214 1071 5 %RANDOM
Rwork0.17656 ---
obs0.17928 20260 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0.53 Å2
2---0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2→21.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 27 124 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132244
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152110
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6463045
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5764822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.34520.992131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37915369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it2.8272.7391089
X-RAY DIFFRACTIONr_mcbond_other2.8212.7371087
X-RAY DIFFRACTIONr_mcangle_it4.1064.0861358
X-RAY DIFFRACTIONr_mcangle_other4.1064.0881359
X-RAY DIFFRACTIONr_scbond_it3.5953.1861155
X-RAY DIFFRACTIONr_scbond_other3.5933.1851156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3934.6491686
X-RAY DIFFRACTIONr_long_range_B_refined7.36932.5862490
X-RAY DIFFRACTIONr_long_range_B_other7.34732.4912474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 61 -
Rwork0.25 1332 -
obs--89.93 %

+
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