[English] 日本語
Yorodumi
- PDB-7awv: Azoreductase (AzoRo) from Rhodococcus opacus 1CP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7awv
TitleAzoreductase (AzoRo) from Rhodococcus opacus 1CP
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase / Actinobacterium / dye degradation / NADH-quinone oxido-reductase
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBento, I. / Ngo, A. / Qi, J. / Juric, C. / Tischler, D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2022
Title: Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase.
Authors: Ngo, A.C.R. / Qi, J. / Juric, C. / Bento, I. / Tischler, D.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,31711
Polymers45,7082
Non-polymers1,6109
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-14 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.652, 140.652, 40.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 3 - 206 / Label seq-ID: 3 - 206

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein FMN-dependent NADH-azoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase / azoreductase-monomer


Mass: 22853.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: azoR, R1CP_39980 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B1KJ01, FMN-dependent NADH-azoreductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16-20% of isopropanol, 12-16% PEG4000 and 0.1M of sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→70.43 Å / Num. obs: 23710 / % possible obs: 99.87 % / Redundancy: 5.6 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.654 / Num. unique obs: 2347 / CC1/2: 0.53 / CC star: 0.832 / Rpim(I) all: 0.795 / Rrim(I) all: 1.84 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.2→70.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.691 / SU ML: 0.256 / Cross valid method: FREE R-VALUE / ESU R: 0.293 / ESU R Free: 0.225
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2611 1221 5.15 %
Rwork0.2161 22488 -
all0.218 --
obs-23709 99.903 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.118 Å2-0.059 Å2-0 Å2
2---0.118 Å20 Å2
3---0.382 Å2
Refinement stepCycle: LAST / Resolution: 2.2→70.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 90 118 3327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133307
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173107
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.6484534
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5647168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.20319.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85315466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023689
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02695
X-RAY DIFFRACTIONr_nbd_refined0.1860.2627
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.22823
X-RAY DIFFRACTIONr_nbtor_refined0.1490.21540
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2136
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.218
X-RAY DIFFRACTIONr_nbd_other0.1570.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.25
X-RAY DIFFRACTIONr_mcbond_it1.472.741663
X-RAY DIFFRACTIONr_mcbond_other1.4682.741662
X-RAY DIFFRACTIONr_mcangle_it2.3094.1042077
X-RAY DIFFRACTIONr_mcangle_other2.314.1052078
X-RAY DIFFRACTIONr_scbond_it1.7462.9361644
X-RAY DIFFRACTIONr_scbond_other1.7462.9371645
X-RAY DIFFRACTIONr_scangle_it2.7724.3242457
X-RAY DIFFRACTIONr_scangle_other2.7724.3252458
X-RAY DIFFRACTIONr_lrange_it5.5352.55314048
X-RAY DIFFRACTIONr_lrange_other5.51652.42813988
X-RAY DIFFRACTIONr_ncsr_local_group_10.1410.056024
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.140970.05007
12BX-RAY DIFFRACTIONLocal ncs0.140970.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.357990.3461656X-RAY DIFFRACTION100
2.257-2.3190.404850.3091575X-RAY DIFFRACTION100
2.319-2.3860.353730.3031617X-RAY DIFFRACTION99.8818
2.386-2.460.368780.2841478X-RAY DIFFRACTION100
2.46-2.540.354840.2921488X-RAY DIFFRACTION99.9364
2.54-2.6290.306760.2721401X-RAY DIFFRACTION100
2.629-2.7290.3860.2511377X-RAY DIFFRACTION100
2.729-2.840.303690.2441330X-RAY DIFFRACTION100
2.84-2.9660.301720.2251259X-RAY DIFFRACTION100
2.966-3.1110.28720.2171233X-RAY DIFFRACTION99.9234
3.111-3.2790.275750.2391137X-RAY DIFFRACTION99.9176
3.279-3.4780.251370.2261127X-RAY DIFFRACTION100
3.478-3.7180.262490.2141037X-RAY DIFFRACTION99.8162
3.718-4.0150.206520.179973X-RAY DIFFRACTION100
4.015-4.3980.247460.155896X-RAY DIFFRACTION99.7881
4.398-4.9160.157530.154788X-RAY DIFFRACTION99.7627
4.916-5.6750.259450.19727X-RAY DIFFRACTION99.8706
5.675-6.9470.284230.196625X-RAY DIFFRACTION99.8459
6.947-9.8080.184380.168475X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.33520.04340.36621.5899-0.70481.9399-0.0027-0.02450.58660.0467-0.00670.128-0.0150.00290.00940.00480.0112-0.00380.0393-0.01380.3403-39.3422-43.7445-0.2622
22.14640.16170.72521.59370.41811.7315-0.19620.48621.1267-0.00610.0023-0.2455-0.16570.25770.1940.0335-0.0382-0.06250.16880.2510.9094-23.2136-28.9696-8.8528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 210
2X-RAY DIFFRACTION1ALLA301
3X-RAY DIFFRACTION1ALLA302
4X-RAY DIFFRACTION1ALLA303
5X-RAY DIFFRACTION1ALLA304
6X-RAY DIFFRACTION1ALLA305
7X-RAY DIFFRACTION1ALLA306
8X-RAY DIFFRACTION2ALLB3 - 207
9X-RAY DIFFRACTION2ALLB301

+
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