[English] 日本語
Yorodumi
- PDB-1gkj: Histidine Ammonia-Lyase (HAL) Mutant Y280F from Pseudomonas putida -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gkj
TitleHistidine Ammonia-Lyase (HAL) Mutant Y280F from Pseudomonas putida
ComponentsHISTIDINE AMMONIA-LYASE
KeywordsLYASE / HISTIDINE DEGRADATION
Function / homology
Function and homology information


histidine ammonia-lyase / histidine ammonia-lyase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / cytoplasm
Similarity search - Function
Histidine ammonia-lyase / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal ...Histidine ammonia-lyase / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine ammonia-lyase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å
AuthorsBaedeker, M. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Structures of Two Histidine Ammonia-Lyase Modifications and Implications for the Catalytic Mechanism
Authors: Baedeker, M. / Schulz, G.E.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile
Authors: Schwede, T.F. / Retey, J. / Schulz, G.E.
History
DepositionAug 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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: HISTIDINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7913
Polymers53,6031
Non-polymers1882
Water6,774376
1
A: HISTIDINE AMMONIA-LYASE
hetero molecules

A: HISTIDINE AMMONIA-LYASE
hetero molecules

A: HISTIDINE AMMONIA-LYASE
hetero molecules

A: HISTIDINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,16612
Polymers214,4134
Non-polymers7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area27470 Å2
ΔGint-214.4 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.560, 116.672, 129.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein HISTIDINE AMMONIA-LYASE / HISTIDASE / HAL


Mass: 53603.223 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP (MDO). THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS ...Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP (MDO). THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS DELETED. THE SIDE CHAIN OF SER 143 IS DEHYDRATED.
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Plasmid: PT7-7H / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P21310, histidine ammonia-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION CYS273ALA, TYR280PHE. THE 3 RESIDUES ALA 142, SER 143 AND GLY 144 ARE ...CHAIN A ENGINEERED MUTATION CYS273ALA, TYR280PHE. THE 3 RESIDUES ALA 142, SER 143 AND GLY 144 ARE LINKED TO GIVE THE MIO 4-METHYLIDENE-IMIDAZOLE-5-ONE SPECIES (MDO) {2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL -1-YL}ACETIC ACID

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growpH: 8.1
Details: CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Crystal grow
*PLUS
pH: 3.85 / Method: vapor diffusion, hanging drop / Details: Schwede, T.F., (1999) Protein Eng., 12, 151.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
21.6 Msodium potassium phosphate1reservoir
30.1 MHEPES1reservoir
41.5 mMEDTA1reservoir
53 %dioxane1reservoirpH3.85

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUB200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19 Å / Num. obs: 64075 / % possible obs: 98 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.6
Reflection
*PLUS
Lowest resolution: 19 Å / % possible obs: 98 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.9

-
Processing

Software
NameClassification
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.7→19 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.236 --
obs0.198 -98 %
all-64075 -
Refinement stepCycle: LAST / Resolution: 1.7→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 11 376 4148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Refinement
*PLUS
Lowest resolution: 19 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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