[English] 日本語
Yorodumi
- PDB-1ahx: ASPARTATE AMINOTRANSFERASE HEXAMUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ahx
TitleASPARTATE AMINOTRANSFERASE HEXAMUTANT
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE (AMINOTRANSFERASE)
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 / 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
HYDROCINNAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMalashkevich, V.N. / Jansonius, J.N.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase.
Authors: Malashkevich, V.N. / Onuffer, J.J. / Kirsch, J.F. / Jansonius, J.N.
#1: Journal: Biochemistry of Vitamin B6 and Pqq / Year: 1994
Title: Redesign of Aspartate Aminotransferase Specificity to that of Tyrosine Aminotransferase
Authors: Kirsch, J.F. / Onuffer, J.J.
History
DepositionFeb 21, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)88,0696
Polymers87,2752
Non-polymers7954
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-14 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.980, 78.690, 89.280
Angle α, β, γ (deg.)90.00, 118.32, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 / 3: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 1.0E-5, 0.00036), (-0.00036, -1, -0.00035), (0.00036, -0.00035, 1)
Vector: 0.04746, 83.63189, 0.02234)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 409 B 5 .. B 409 0.185

-
Components

#1: Protein ASPARTATE AMINOTRANSFERASE / ASPARTATE TRANSAMINASE


Mass: 43637.293 Da / Num. of mol.: 2 / Mutation: V39L, K41Y, T47I, N69L, T109S, N297S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND SUBSTRATE SPECIFICITY CHANGED TO THAT OF TYROSINE AMINOTRANSFERASE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
220 mMpotassium phosphate1drop
30.01 mMPLP1drop
42 mMEDTA1drop
50.5 mMDTT1drop
61.90-1.95 Mammonium sulfate1reservoir
7200 mMN-methylmorpholine1reservoir
82 %PEG4001reservoir

-
Data collection

Diffraction sourceWavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.092
Reflection
*PLUS
Num. obs: 65594 / % possible obs: 90.6 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.092

-
Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection% reflection
obs0.226 62465 93.5 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 52 529 6723
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01363200.02
X-RAY DIFFRACTIONt_angle_deg2.985343
X-RAY DIFFRACTIONt_dihedral_angle_d24.9375215
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0061720.02
X-RAY DIFFRACTIONt_gen_planes0.0119240.02
X-RAY DIFFRACTIONt_it3.4467350.2
X-RAY DIFFRACTIONt_nbd0.0181960.1

+
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