[English] 日本語
Yorodumi
- PDB-5ax8: Recombinant expression, purification and preliminary crystallogra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ax8
TitleRecombinant expression, purification and preliminary crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase
ComponentsAspartate aminotransferase, mitochondrialAspartate transaminase
KeywordsTRANSFERASE / aspartate aminotransferase / plasma membrane fatty acid binding protein / kynurenine aminotransferase-IV / three-dimensional structure
Function / homology
Function and homology information


4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate biosynthetic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / Aspartate and asparagine metabolism / glutamate metabolic process ...4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate biosynthetic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / Aspartate and asparagine metabolism / glutamate metabolic process / Glutamate and glutamine metabolism / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / Glyoxylate metabolism and glycine degradation / Gluconeogenesis / fatty acid transport / pyridoxal phosphate binding / response to ethanol / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / plasma membrane
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsJiang, X. / Wang, J. / Chang, H. / Zhou, Y.
CitationJournal: Biosci Trends / Year: 2016
Title: Recombinant expression, purification and crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase
Authors: Jiang, X. / Wang, J. / Chang, H. / Zhou, Y.
History
DepositionJul 20, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
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


Theoretical massNumber of molelcules
Total (without water)182,3324
Polymers182,3324
Non-polymers00
Water0
1
A: Aspartate aminotransferase, mitochondrial
C: Aspartate aminotransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)91,1662
Polymers91,1662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-26 kcal/mol
Surface area30720 Å2
MethodPISA
2
B: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)91,1662
Polymers91,1662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-25 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.706, 76.140, 94.247
Angle α, β, γ (deg.)78.00, 85.65, 78.41
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Aspartate aminotransferase, mitochondrial / Aspartate transaminase / mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Kynurenine ...mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Kynurenine aminotransferase 4 / Kynurenine aminotransferase IV / Kynurenine--oxoglutarate transaminase 4 / Kynurenine--oxoglutarate transaminase IV / Plasma membrane-associated fatty acid-binding protein / FABPpm / Transaminase A


Mass: 45583.086 Da / Num. of mol.: 4 / Fragment: UNP residues 40-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT2 / Plasmid: pET22b-hmAspAT / Production host: Escherichia coli (E. coli)
References: UniProt: P00505, aspartate transaminase, kynurenine-oxoglutarate transaminase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M HEPES pH 6.8, 25% (v/v) Jeffamine ED-2001 pH 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.989→50 Å / Num. obs: 30161 / % possible obs: 97.2 % / Redundancy: 1.9 % / Rsym value: 0.083 / Net I/σ(I): 4.3
Reflection shellResolution: 2.989→3.05 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.265 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PDB

3pdb


Resolution: 2.989→48.315 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2913 2000 7.42 %
Rwork0.2726 --
obs0.274 26959 88.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.989→48.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 0 0 12580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01812872
X-RAY DIFFRACTIONf_angle_d1.71517392
X-RAY DIFFRACTIONf_dihedral_angle_d17.9634768
X-RAY DIFFRACTIONf_chiral_restr0.111868
X-RAY DIFFRACTIONf_plane_restr0.012256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9894-3.06420.3087770.3639957X-RAY DIFFRACTION47
3.0642-3.1470.32771080.36541351X-RAY DIFFRACTION66
3.147-3.23960.35391220.33751527X-RAY DIFFRACTION77
3.2396-3.34410.31621440.32461789X-RAY DIFFRACTION88
3.3441-3.46360.32071500.31841888X-RAY DIFFRACTION94
3.4636-3.60220.30071550.30111930X-RAY DIFFRACTION95
3.6022-3.76610.29071550.28321922X-RAY DIFFRACTION96
3.7661-3.96460.31111520.27961904X-RAY DIFFRACTION95
3.9646-4.21280.2971580.26871958X-RAY DIFFRACTION97
4.2128-4.53790.27661550.26081955X-RAY DIFFRACTION97
4.5379-4.99420.27931560.24181940X-RAY DIFFRACTION96
4.9942-5.71580.32531550.26051927X-RAY DIFFRACTION95
5.7158-7.19750.28081590.25491983X-RAY DIFFRACTION98
7.1975-48.32140.23311540.22141928X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 26.5849 Å / Origin y: -16.4266 Å / Origin z: -62.0946 Å
111213212223313233
T0.3833 Å2-0.0519 Å2-0.0308 Å2-0.3439 Å2-0.0362 Å2--0.4023 Å2
L0.1321 °2-0.1973 °20.1178 °2-0.7339 °2-0.6796 °2--0.5422 °2
S0.0858 Å °0.0881 Å °-0.0867 Å °-0.2171 Å °-0.0288 Å °0.1135 Å °0.2062 Å °0.0245 Å °-0.0625 Å °
Refinement TLS groupSelection details: all

+
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