[English] 日本語
Yorodumi
- PDB-8e9d: Crystal structure of E. coli aspartate aminotransferase mutant AI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8e9d
TitleCrystal structure of E. coli aspartate aminotransferase mutant AIFS bound to maleic acid at 100 K
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / Enzyme / Designed Protein / Mutant Protein
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsChica, R.A. / St-Jacques, A.D. / Rodriguez, J.M. / Thompson, M.C.
Funding support Canada, United States, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04831 Canada
Ontario Early Researcher AwardsER14-10-139 Canada
Canada Foundation for Innovation26503 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124169 United States
CitationJournal: Nat Commun / Year: 2023
Title: Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.
Authors: St-Jacques, A.D. / Rodriguez, J.M. / Eason, M.G. / Foster, S.M. / Khan, S.T. / Damry, A.M. / Goto, N.K. / Thompson, M.C. / Chica, R.A.
History
DepositionAug 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2296
Polymers89,5032
Non-polymers7264
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-16 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.220, 141.220, 81.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

#1: Protein Aspartate aminotransferase / AspAT / Transaminase A


Mass: 44751.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC, b0928, JW0911 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, maleate, ammonium sulfate, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.37→61.15 Å / Num. obs: 188377 / % possible obs: 97.7 % / Redundancy: 19.8 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.9
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 17.3 % / Rmerge(I) obs: 1.657 / Num. unique obs: 8826 / CC1/2: 0.59 / Rpim(I) all: 0.399 / Rrim(I) all: 1.707 / Net I/σ(I) obs: 1.7 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X28

1x28


Resolution: 1.37→61.15 Å / SU ML: 0.1405 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.4905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1604 18994 10.08 %
Rwork0.1487 169364 -
obs0.1499 188358 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.64 Å2
Refinement stepCycle: LAST / Resolution: 1.37→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6178 0 16 742 6936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01156739
X-RAY DIFFRACTIONf_angle_d1.22459215
X-RAY DIFFRACTIONf_chiral_restr0.0811003
X-RAY DIFFRACTIONf_plane_restr0.00961250
X-RAY DIFFRACTIONf_dihedral_angle_d21.53982466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.30925910.28995231X-RAY DIFFRACTION90.86
1.39-1.40.26216130.25025442X-RAY DIFFRACTION94.7
1.4-1.420.23776160.2275496X-RAY DIFFRACTION95.96
1.42-1.440.22796180.20985526X-RAY DIFFRACTION95.91
1.44-1.460.21686320.19115586X-RAY DIFFRACTION96.25
1.46-1.480.20896200.18465539X-RAY DIFFRACTION96.35
1.48-1.50.20546180.17265537X-RAY DIFFRACTION96.61
1.5-1.520.18356270.1685581X-RAY DIFFRACTION96.79
1.52-1.540.19036230.16135586X-RAY DIFFRACTION96.96
1.54-1.570.17416290.15345589X-RAY DIFFRACTION96.75
1.57-1.60.17396270.15165617X-RAY DIFFRACTION97.05
1.6-1.620.16826270.1475572X-RAY DIFFRACTION97.25
1.62-1.660.16886380.14515647X-RAY DIFFRACTION97.58
1.66-1.690.16916310.14665621X-RAY DIFFRACTION97.78
1.69-1.730.15736320.14535638X-RAY DIFFRACTION97.74
1.73-1.770.16816330.14115644X-RAY DIFFRACTION97.83
1.77-1.810.16576390.14165700X-RAY DIFFRACTION98.19
1.81-1.860.16626350.14225656X-RAY DIFFRACTION98.36
1.86-1.910.17896380.14935667X-RAY DIFFRACTION98.25
1.91-1.980.17066390.14535673X-RAY DIFFRACTION98.35
1.98-2.050.16256330.14855732X-RAY DIFFRACTION98.87
2.05-2.130.16796350.14325713X-RAY DIFFRACTION98.83
2.13-2.230.15666800.13865713X-RAY DIFFRACTION99.16
2.23-2.340.14346160.13375741X-RAY DIFFRACTION99.06
2.34-2.490.14386260.13275782X-RAY DIFFRACTION99.36
2.49-2.680.166390.14225794X-RAY DIFFRACTION99.57
2.68-2.950.1566820.14755760X-RAY DIFFRACTION99.6
2.95-3.380.15416650.15525783X-RAY DIFFRACTION99.83
3.38-4.260.14556340.14025857X-RAY DIFFRACTION99.88
4.26-61.150.14816580.14975941X-RAY DIFFRACTION99.88

+
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