[English] 日本語
Yorodumi
- PDB-7bx9: Purification, characterization and X-ray structure of YhdA-type a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bx9
TitlePurification, characterization and X-ray structure of YhdA-type azoreductase from Bacillus velezensis
ComponentsAzoreductase
KeywordsOXIDOREDUCTASE / Azo reductase / Azr / FMN / FLAVOPROTEIN
Function / homology: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / nucleotide binding / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Azoreductase
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsKhan, F. / Suguna, K.
CitationJournal: Proteins / Year: 2021
Title: Purification, characterization, and crystal structure of YhdA-type azoreductase from Bacillus velezensis.
Authors: Bafana, A. / Khan, F. / Suguna, K.
History
DepositionApr 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6448
Polymers18,6321
Non-polymers1,0127
Water3,963220
1
A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57732
Polymers74,5304
Non-polymers4,04728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area17710 Å2
ΔGint-79 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 102.470, 65.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-362-

HOH

31A-378-

HOH

41A-446-

HOH

51A-479-

HOH

61A-481-

HOH

71A-511-

HOH

81A-514-

HOH

91A-519-

HOH

-
Components

#1: Protein Azoreductase


Mass: 18632.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: azr / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: B3VPZ9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.05 M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→36.71 Å / Num. obs: 51008 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 11.69 Å2 / CC1/2: 0.996 / Net I/σ(I): 10
Reflection shellResolution: 1.38→1.41 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2504 / CC1/2: 0.792

-
Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSW

2gsw


Resolution: 1.38→30.97 Å / SU ML: 0.1158 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.2304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1515 2693 5.28 %
Rwork0.1306 48313 -
obs0.1317 51006 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.53 Å2
Refinement stepCycle: LAST / Resolution: 1.38→30.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 66 220 1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471407
X-RAY DIFFRACTIONf_angle_d0.77561897
X-RAY DIFFRACTIONf_chiral_restr0.0711208
X-RAY DIFFRACTIONf_plane_restr0.0053236
X-RAY DIFFRACTIONf_dihedral_angle_d12.6764843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.26581530.20632504X-RAY DIFFRACTION99.96
1.41-1.430.16281390.16632515X-RAY DIFFRACTION100
1.43-1.460.18841250.14372539X-RAY DIFFRACTION100
1.46-1.50.15391620.13412478X-RAY DIFFRACTION99.96
1.5-1.530.15691350.12122515X-RAY DIFFRACTION100
1.53-1.570.14511400.11732544X-RAY DIFFRACTION100
1.57-1.610.12691390.1112502X-RAY DIFFRACTION100
1.61-1.660.16071420.11462537X-RAY DIFFRACTION99.89
1.66-1.710.13081370.11492527X-RAY DIFFRACTION99.81
1.71-1.770.14371590.11772479X-RAY DIFFRACTION99.89
1.77-1.840.16531350.12212539X-RAY DIFFRACTION99.78
1.84-1.930.15021520.1182536X-RAY DIFFRACTION99.93
1.93-2.030.1331390.11862545X-RAY DIFFRACTION100
2.03-2.160.1511400.11842531X-RAY DIFFRACTION100
2.16-2.320.13671420.1242556X-RAY DIFFRACTION100
2.32-2.560.15811210.12752579X-RAY DIFFRACTION100
2.56-2.930.1431490.13892570X-RAY DIFFRACTION100
2.93-3.690.15311440.1252606X-RAY DIFFRACTION100
3.69-30.970.15481400.15022711X-RAY DIFFRACTION99.65

+
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