[English] 日本語
Yorodumi
- PDB-7bgm: Crystal structure of MtHISN2, a bifunctional enzyme from the hist... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bgm
TitleCrystal structure of MtHISN2, a bifunctional enzyme from the histidine biosynthetic pathway
ComponentsPhosphoribosyl-AMP cyclohydrolase
KeywordsHYDROLASE / Histidine / Pyrophosphohydrolase / Cyclohydrolase / Bifunctional / PRA-CH / PRA-PH
Function / homology
Function and homology information


phosphoribosyl-AMP cyclohydrolase activity / phosphoribosyl-ATP diphosphatase activity / Hydrolases / L-histidine biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosyl-AMP cyclohydrolase domain / Phosphoribosyl-AMP cyclohydrolase domain superfamily / Phosphoribosyl-AMP cyclohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase
Similarity search - Domain/homology
Histidine biosynthesis hisIE protein
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWitek, W. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Sci Rep / Year: 2021
Title: Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants.
Authors: Witek, W. / Sliwiak, J. / Ruszkowski, M.
History
DepositionJan 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoribosyl-AMP cyclohydrolase
B: Phosphoribosyl-AMP cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,97311
Polymers53,3842
Non-polymers5899
Water6,413356
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-353 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.422, 69.477, 52.130
Angle α, β, γ (deg.)90.000, 94.696, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-423-

HOH

-
Components

#1: Protein Phosphoribosyl-AMP cyclohydrolase


Mass: 26692.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Without a signal peptide (residues 1-48) / Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25498966, MTR_7g084480, MtrunA17_Chr7g0252441 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A072U2X9, phosphoribosyl-AMP cyclohydrolase, phosphoribosyl-ATP diphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol) 0.1 M Buffer System 1 , pH 6.5 (Imidazole; MES-acid) ...Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol) 0.1 M Buffer System 1 , pH 6.5 (Imidazole; MES-acid) 30% Precipitant Mix 1 (20% v/v PEG 500* MME; 10 % w/v PEG 20000. Cryoprotection: 20% ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→80 Å / Num. obs: 79751 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12569 / CC1/2: 0.69 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Cootmodel building
PHENIXAutobuildmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.93 Å / SU ML: 0.155 / Cross valid method: FREE R-VALUE / Phase error: 18.9436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 1037 1.3 %
Rwork0.1434 78701 -
obs0.1439 79738 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 9 356 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063381
X-RAY DIFFRACTIONf_angle_d1.01384571
X-RAY DIFFRACTIONf_chiral_restr0.0589539
X-RAY DIFFRACTIONf_plane_restr0.0063582
X-RAY DIFFRACTIONf_dihedral_angle_d14.70731250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.27261440.213410926X-RAY DIFFRACTION95.92
1.68-1.790.20541480.168911242X-RAY DIFFRACTION98.91
1.79-1.930.20821480.148911278X-RAY DIFFRACTION99.12
1.93-2.120.19281480.127711234X-RAY DIFFRACTION99.15
2.12-2.430.16171490.126311259X-RAY DIFFRACTION98.92
2.43-3.060.1731490.149711323X-RAY DIFFRACTION98.86
3.06-42.930.16261510.141511439X-RAY DIFFRACTION98.72

+
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