[English] 日本語
Yorodumi
- PDB-3hlm: Crystal Structure of Mouse Mitochondrial Aspartate Aminotransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hlm
TitleCrystal Structure of Mouse Mitochondrial Aspartate Aminotransferase/Kynurenine Aminotransferase IV
ComponentsAspartate aminotransferase, mitochondrial
KeywordsTRANSFERASE / ALPHA & BETA PROTEIN / PLP-DEPENDENT TRANSFERASE / AMINOTRANSFERASE / MULTIFUNCTIONAL ENZYME / PYRIDOXAL PHOSPHATE / Acetylation / Cell membrane / Lipid transport / Membrane / Mitochondrion / Nitration / Phosphoprotein / Transit peptide / Transport
Function / homology
Function and homology information


Malate-aspartate shuttle / Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / Glyoxylate metabolism and glycine degradation / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity ...Malate-aspartate shuttle / Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / Glyoxylate metabolism and glycine degradation / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / carboxylic acid binding / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / amino acid binding / fatty acid transport / T-tubule / phospholipid binding / sarcolemma / pyridoxal phosphate binding / myelin sheath / perikaryon / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / enzyme binding / cell surface / protein-containing complex / mitochondrion / identical protein binding
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHan, Q. / Robinson, H. / Li, J.
CitationJournal: Cell.Mol.Life Sci. / Year: 2010
Title: Structure, expression, and function of kynurenine aminotransferases in human and rodent brains.
Authors: Han, Q. / Cai, T. / Tagle, D.A. / Li, J.
History
DepositionMay 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
C: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,01710
Polymers179,4644
Non-polymers5536
Water11,764653
1
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1937
Polymers89,7322
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-22 kcal/mol
Surface area30750 Å2
MethodPISA
2
C: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8243
Polymers89,7322
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-22 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.322, 76.792, 87.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Aspartate aminotransferase, mitochondrial / mAspAT / Transaminase A / Glutamate oxaloacetate transaminase 2 / Fatty acid-binding protein / FABP-1 / FABPpm


Mass: 44866.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Got-2, Got2 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05202, aspartate transaminase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 100 mM Ammonium Sulphate, 6% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007 / Details: SI 111 Channel
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.5→29.9 Å / Num. obs: 67188 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 9AAT

9aat


Resolution: 2.5→29.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / ESU R: 0.729 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23429 3126 5 %RANDOM
Rwork0.18089 ---
obs0.18354 58833 92.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.137 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 36 653 13309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02212946
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.95917494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82151600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37323.889576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.333152220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7171580
X-RAY DIFFRACTIONr_chiral_restr0.1390.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219816
X-RAY DIFFRACTIONr_mcbond_it1.0041.57960
X-RAY DIFFRACTIONr_mcangle_it1.854212784
X-RAY DIFFRACTIONr_scbond_it3.06634986
X-RAY DIFFRACTIONr_scangle_it4.8314.54710
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 115 -
Rwork0.298 2388 -
obs--51.29 %

+
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://pdbjlc1.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