[English] 日本語
Yorodumi
- PDB-2huf: Crystal structure of Aedes aegypti alanine glyoxylate aminotransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2huf
TitleCrystal structure of Aedes aegypti alanine glyoxylate aminotransferase
ComponentsAlanine glyoxylate aminotransferase
KeywordsTRANSFERASE / Alpha and beta protein / PLP-dependent transferase
Function / homology
Function and homology information


alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / L-serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding / peroxisome
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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
1-BUTANOL / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHan, Q. / Robinson, H. / Gao, Y.G. / Vogelaar, N. / Wilson, S.R. / Rizzi, M. / Li, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structures of Aedes aegypti Alanine Glyoxylate Aminotransferase.
Authors: Han, Q. / Robinson, H. / Gao, Y.G. / Vogelaar, N. / Wilson, S.R. / Rizzi, M. / Li, J.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 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: Alanine glyoxylate aminotransferase
B: Alanine glyoxylate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9304
Polymers86,7822
Non-polymers1482
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-29 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.964, 136.964, 120.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Alanine glyoxylate aminotransferase


Mass: 43390.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Plasmid: pBlueBac4.5 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q3LSM4, alanine-glyoxylate transaminase
#2: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 8000, 0.13 M magnesium acetate, 4% butanol, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2006
RadiationMonochromator: Si(111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 84787 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.75→1.81 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1h0c

1h0c


Resolution: 1.75→29.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.903 / SU ML: 0.063 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20291 4233 5 %RANDOM
Rwork0.17222 ---
all0.17374 80543 --
obs0.17374 84776 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.577 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 10 520 6486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226096
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9768270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07623.12250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.157151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.561546
X-RAY DIFFRACTIONr_chiral_restr0.180.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024580
X-RAY DIFFRACTIONr_nbd_refined0.2190.23203
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2520
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.26
X-RAY DIFFRACTIONr_mcbond_it0.9871.53911
X-RAY DIFFRACTIONr_mcangle_it1.32426136
X-RAY DIFFRACTIONr_scbond_it2.31132474
X-RAY DIFFRACTIONr_scangle_it3.5844.52134
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 331 -
Rwork0.204 5884 -
obs--99.81 %

+
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