[English] 日本語
Yorodumi
- PDB-6dna: Crystal structure of T110A mutant human Glutamate oxaloacetate tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dna
TitleCrystal structure of T110A mutant human Glutamate oxaloacetate transaminase 1 (GOT1)
ComponentsAspartate aminotransferase, cytoplasmicAspartate transaminase
KeywordsTRANSFERASE / Aspartate aminotransferase / Glutamate oxaloacetate transaminase 1 / GOT1 / PLP
Function / homology
Function and homology information


phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process ...phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / 2-oxoglutarate metabolic process / oxaloacetate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / Gluconeogenesis / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytosol / cytoplasm
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 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 ...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 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAssar, Z. / Holt, M.C. / Stein, A.J. / Lairson, L. / Lyssiotis, C.A.
CitationJournal: Biochemistry / Year: 2018
Title: Biochemical Characterization and Structure-Based Mutational Analysis Provide Insight into the Binding and Mechanism of Action of Novel Aspartate Aminotransferase Inhibitors.
Authors: Holt, M.C. / Assar, Z. / Beheshti Zavareh, R. / Lin, L. / Anglin, J. / Mashadova, O. / Haldar, D. / Mullarky, E. / Kremer, D.M. / Cantley, L.C. / Kimmelman, A.C. / Stein, A.J. / Lairson, L.L. / Lyssiotis, C.A.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate aminotransferase, cytoplasmic
B: Aspartate aminotransferase, cytoplasmic
C: Aspartate aminotransferase, cytoplasmic
D: Aspartate aminotransferase, cytoplasmic
E: Aspartate aminotransferase, cytoplasmic
F: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,78015
Polymers274,7146
Non-polymers2,0669
Water1629
1
A: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2273
Polymers45,7861
Non-polymers4412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2273
Polymers45,7861
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0332
Polymers45,7861
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2273
Polymers45,7861
Non-polymers4412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0332
Polymers45,7861
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0332
Polymers45,7861
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)257.700, 148.626, 83.183
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTHRTHRAA16 - 41011 - 405
21VALVALTHRTHRBB16 - 41011 - 405
12VALVALALAALAAA16 - 40211 - 397
22VALVALALAALACC16 - 40211 - 397
13VALVALTHRTHRAA16 - 41011 - 405
23VALVALTHRTHRDD16 - 41011 - 405
14LEULEUVALVALAA17 - 40912 - 404
24LEULEUVALVALEE17 - 40912 - 404
15VALVALLEULEUAA16 - 39811 - 393
25VALVALLEULEUFF16 - 39811 - 393
16PROPROALAALABB15 - 40210 - 397
26PROPROALAALACC15 - 40210 - 397
17PROPROTHRTHRBB15 - 41010 - 405
27PROPROTHRTHRDD15 - 41010 - 405
18LEULEUALAALABB17 - 40812 - 403
28LEULEUALAALAEE17 - 40812 - 403
19VALVALLEULEUBB16 - 39811 - 393
29VALVALLEULEUFF16 - 39811 - 393
110GLNGLNALAALACC14 - 4029 - 397
210GLNGLNALAALADD14 - 4029 - 397
111LEULEUALAALACC17 - 40212 - 397
211LEULEUALAALAEE17 - 40212 - 397
112VALVALLEULEUCC16 - 39811 - 393
212VALVALLEULEUFF16 - 39811 - 393
113LEULEUALAALADD17 - 40812 - 403
213LEULEUALAALAEE17 - 40812 - 403
114VALVALLEULEUDD16 - 39811 - 393
214VALVALLEULEUFF16 - 39811 - 393
115LEULEULEULEUEE17 - 39812 - 393
215LEULEULEULEUFF17 - 39812 - 393

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Aspartate aminotransferase, cytoplasmic / Aspartate transaminase / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 45785.703 Da / Num. of mol.: 6 / Mutation: T110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P17174, aspartate transaminase, cysteine transaminase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 3,350, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 4281 / % possible obs: 99.77 % / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.42
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.61

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3II0

3ii0


Resolution: 3→48.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.869 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21144 3047 4.9 %RANDOM
Rwork0.18402 ---
obs0.18538 59473 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20.19 Å2
2--0.43 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 3→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18277 0 132 9 18418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01418990
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716549
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.65825850
X-RAY DIFFRACTIONr_angle_other_deg0.8881.63738674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95352372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80622.1251012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.584152930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.17515125
X-RAY DIFFRACTIONr_chiral_restr0.0690.22425
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023707
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_it8.017.6829431
X-RAY DIFFRACTIONr_mcbond_other8.017.6829430
X-RAY DIFFRACTIONr_mcangle_it12.31411.50811783
X-RAY DIFFRACTIONr_mcangle_other12.31311.50811784
X-RAY DIFFRACTIONr_scbond_it6.8317.7729559
X-RAY DIFFRACTIONr_scbond_other6.837.7729560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.36611.6114055
X-RAY DIFFRACTIONr_long_range_B_refined20.40779196
X-RAY DIFFRACTIONr_long_range_B_other20.40779197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A116230.13
12B116230.13
21A115010.13
22C115010.13
31A115960.14
32D115960.14
41A115260.14
42E115260.14
51A113030.14
52F113030.14
61B116500.13
62C116500.13
71B116860.14
72D116860.14
81B118220.13
82E118220.13
91B115520.14
92F115520.14
101C117930.13
102D117930.13
111C118440.13
112E118440.13
121C117410.13
122F117410.13
131D116930.14
132E116930.14
141D117100.13
142F117100.13
151E114810.14
152F114810.14
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 219 -
Rwork0.218 4364 -
obs--99.11 %

+
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