[English] 日本語
Yorodumi
- PDB-4atq: GABA-transaminase A1R958 in complex with external aldimine PLP-GA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4atq
TitleGABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct
Components4-AMINOBUTYRATE TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


(S)-3-amino-2-methylpropionate transaminase activity / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...4-aminobutyrate aminotransferase, bacterial / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
GAMMA-AMINO-BUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate aminotransferase
Similarity search - Component
Biological speciesARTHROBACTER AURESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBruce, H. / Tuan, A.N. / Mangas Sanchez, J. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of a Gamma-Aminobutyrate (Gaba) Transaminase from the S-Triazine-Degrading Organism Arthrobacter Aurescens Tc1 in Complex with Plp and with its External Aldimine Plp- Gaba Adduct.
Authors: Bruce, H. / Nguyen Tuan, A. / Mangas Sanchez, J. / Leese, C. / Hopwood, J. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMay 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-AMINOBUTYRATE TRANSAMINASE
B: 4-AMINOBUTYRATE TRANSAMINASE
C: 4-AMINOBUTYRATE TRANSAMINASE
D: 4-AMINOBUTYRATE TRANSAMINASE
E: 4-AMINOBUTYRATE TRANSAMINASE
F: 4-AMINOBUTYRATE TRANSAMINASE
G: 4-AMINOBUTYRATE TRANSAMINASE
H: 4-AMINOBUTYRATE TRANSAMINASE
I: 4-AMINOBUTYRATE TRANSAMINASE
J: 4-AMINOBUTYRATE TRANSAMINASE
K: 4-AMINOBUTYRATE TRANSAMINASE
L: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)575,81236
Polymers571,60912
Non-polymers4,20324
Water9,836546
1
A: 4-AMINOBUTYRATE TRANSAMINASE
B: 4-AMINOBUTYRATE TRANSAMINASE
C: 4-AMINOBUTYRATE TRANSAMINASE
D: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26260 Å2
ΔGint-120.3 kcal/mol
Surface area49870 Å2
MethodPISA
2
E: 4-AMINOBUTYRATE TRANSAMINASE
F: 4-AMINOBUTYRATE TRANSAMINASE
G: 4-AMINOBUTYRATE TRANSAMINASE
H: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26200 Å2
ΔGint-124.1 kcal/mol
Surface area49430 Å2
MethodPISA
3
I: 4-AMINOBUTYRATE TRANSAMINASE
J: 4-AMINOBUTYRATE TRANSAMINASE
K: 4-AMINOBUTYRATE TRANSAMINASE
L: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25950 Å2
ΔGint-129 kcal/mol
Surface area49570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.710, 292.830, 105.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
4-AMINOBUTYRATE TRANSAMINASE / A1R958 TRANSAMINASE


Mass: 47634.102 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN SIDE CHAN OF LYS295 AND ALDEHYDIC CARBON OF PLP
Source: (gene. exp.) ARTHROBACTER AURESCENS (bacteria) / Strain: TC1 / Description: GENOMIC DNA FROM ATCC / Plasmid: PET-YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1R958, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE (PLP-ABU): PLP-GABA ADDUCT
Sequence detailsUNIPROT SUGGESTS ALA AT POSITION 113 BUT DENSITY STRONGLY SUGGESTS THR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5
Details: 28% (W/V) PEG3350, 0.2M AMMONIUM ACETATE, 1MM PLP, 3% (V/V) DIOXANE, 10 MM GABA, 100 MM BIS-TRIS PROPANE PH 7.5, PROTEIN AT 10 MG PER ML.

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→97.61 Å / Num. obs: 136067 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ATP

4atp


Resolution: 2.75→90.87 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.913 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24803 7182 5 %RANDOM
Rwork0.20177 ---
obs0.20407 136067 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.75→90.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37887 0 264 546 38697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01938980
X-RAY DIFFRACTIONr_bond_other_d0.0080.0225119
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.96853101
X-RAY DIFFRACTIONr_angle_other_deg1.3853.00161480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60855264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71123.9381460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.863155655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.53315228
X-RAY DIFFRACTIONr_chiral_restr0.0820.26167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02144752
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027617
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 495 -
Rwork0.299 9455 -
obs--99.99 %

+
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