[English] 日本語
Yorodumi
- PDB-6hnd: Crystal structure of the aromatic aminotransferase Aro9 from C. A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hnd
TitleCrystal structure of the aromatic aminotransferase Aro9 from C. Albicans
ComponentsAromatic-amino-acid:2-oxoglutarate transaminase
KeywordsTRANSFERASE / Aro9 from C. Albicans
Function / homology
Function and homology information


aromatic-amino-acid transaminase activity / L-lysine catabolic process / 2-aminoadipate transaminase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / aromatic amino acid family catabolic process / L-tyrosine biosynthetic process / L-lysine biosynthetic process via aminoadipic acid / L-phenylalanine biosynthetic process / aromatic amino acid family biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / Aromatic-amino-acid:2-oxoglutarate transaminase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKiliszek, A. / Rzad, K. / Rypniewski, W. / Milewski, S. / Gabriel, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
2015/17/B/NZ6/04248 Poland
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties.
Authors: Kiliszek, A. / Rypniewski, W. / Rzad, K. / Milewski, S. / Gabriel, I.
History
DepositionSep 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aromatic-amino-acid:2-oxoglutarate transaminase
B: Aromatic-amino-acid:2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1947
Polymers119,4242
Non-polymers7705
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-73 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.377, 89.285, 161.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Aromatic-amino-acid:2-oxoglutarate transaminase


Mass: 59712.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ARO9, orf19.1237, CAALFM_C405560CA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1D8PMC5
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.06 M MgCl2, 0.06 M CaCl2, 0.1 M Tris (base): BICINE pH 8.5, 12.5% v/v MPD, 12.5% PEG 1000, 12.5% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.89429 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 53903 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 11.3
Reflection shellResolution: 2.23→2.36 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 8523 / CC1/2: 0.788 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JE5

4je5


Resolution: 2.23→46.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.999 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 2696 5 %RANDOM
Rwork0.16891 ---
obs0.17193 51206 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.075 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2---0.36 Å20 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.23→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7557 0 47 520 8124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137797
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177190
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.64510588
X-RAY DIFFRACTIONr_angle_other_deg1.2711.57916700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00423.243407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.667151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4181534
X-RAY DIFFRACTIONr_chiral_restr0.0710.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021641
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_it3.1624.1433740
X-RAY DIFFRACTIONr_mcbond_other3.164.1423739
X-RAY DIFFRACTIONr_mcangle_it4.4896.194661
X-RAY DIFFRACTIONr_mcangle_other4.4896.1914662
X-RAY DIFFRACTIONr_scbond_it3.8754.5594057
X-RAY DIFFRACTIONr_scbond_other3.8744.564058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8216.6825928
X-RAY DIFFRACTIONr_long_range_B_refined7.39548.3338794
X-RAY DIFFRACTIONr_long_range_B_other7.40148.1728709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.264 3678 -
obs--98.2 %

+
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