[English] 日本語
Yorodumi
- PDB-4m0c: The crystal structure of a FMN-dependent NADH-azoreductase from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m0c
TitleThe crystal structure of a FMN-dependent NADH-azoreductase from Bacillus anthracis str. Ames Ancestor in complex with FMN.
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
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 / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-dependent NADH:quinone oxidoreductase 1
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus anthracis str. Ames Ancestor in complex with FMN.
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2889
Polymers51,9952
Non-polymers1,2937
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-95 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.483, 88.709, 98.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted to be dimeric.

-
Components

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


Mass: 25997.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: azoR1,BAS0908, BA_0966, GBAA_0966 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q81UB2, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Zinc Acetate, 0.1M Imidazole:HCl, 10% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2012 / Details: mirror
RadiationMonochromator: SI 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.073→33 Å / Num. all: 26228 / Num. obs: 26228 / % possible obs: 99.4 % / Observed criterion σ(F): -5 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.2
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1288 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U7I

3u7i


Resolution: 2.073→32.726 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1325 5.06 %random
Rwork0.1758 ---
all0.1783 26175 --
obs0.1783 26175 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.073→32.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 77 109 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083502
X-RAY DIFFRACTIONf_angle_d1.0564744
X-RAY DIFFRACTIONf_dihedral_angle_d14.0741290
X-RAY DIFFRACTIONf_chiral_restr0.075538
X-RAY DIFFRACTIONf_plane_restr0.004591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.073-2.1560.30821490.23242656X-RAY DIFFRACTION97
2.156-2.25410.27531200.20882717X-RAY DIFFRACTION99
2.2541-2.37290.26851430.19052728X-RAY DIFFRACTION99
2.3729-2.52150.23961580.18832731X-RAY DIFFRACTION99
2.5215-2.71610.27241300.19252748X-RAY DIFFRACTION100
2.7161-2.98930.25011600.18452759X-RAY DIFFRACTION100
2.9893-3.42150.24661560.17832767X-RAY DIFFRACTION100
3.4215-4.30910.19531600.152794X-RAY DIFFRACTION100
4.3091-32.72980.17451490.16462950X-RAY DIFFRACTION99
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)
15.78740.4945-2.53171.7955-0.05022.7397-0.12130.2138-0.3527-0.02190.1331-0.04310.1496-0.20190.04720.2803-0.0035-0.02730.19890.0140.276112.7597-13.2346-11.5024
22.59490.2955-0.34781.48950.55872.598-0.0028-0.15880.0659-0.05890.00390.063-0.0987-0.1826-0.02580.16790.0276-0.01260.18540.02440.18878.6139-3.2425-12.673
34.55291.15251.38375.2174-0.3946.7207-0.02930.1151-0.0891-0.12730.0323-0.26670.40860.6161-0.19430.19490.04940.00390.2807-0.00220.278836.04334.4959-19.182
45.95953.11582.47557.11041.19946.3773-0.20640.40490.1286-0.09990.1928-0.8673-0.34371.15240.09440.244-0.01170.03410.37330.09810.394139.859812.4297-23.9478
53.26460.6664-2.83463.0257-3.17215.14460.0058-0.37360.02050.2047-0.4205-0.5803-0.14440.32180.32130.23090.034-0.07520.2774-0.04860.346437.22233.5667-10.514
68.9146-2.71641.45826.86170.58482.0099-0.0316-1.15110.09850.54390.2583-0.03830.1678-0.6577-0.30360.37760.0456-0.03560.4620.00440.251926.0921-6.21729.5955
72.92090.864-1.28038.5538-6.84467.7032-0.1064-0.2072-0.19370.4898-0.097-0.4209-0.06030.60170.17290.26950.0233-0.05740.3552-0.05090.268834.7746-0.32991.2298
83.74540.1521.21862.98450.2554.7132-0.1241-0.39290.10010.44860.0686-0.1526-0.1513-0.10210.09550.22640.0329-0.02620.1827-0.03290.221126.70057.0338-7.9894
92.06660.4259-0.31082.9306-0.24175.4587-0.1008-0.50240.5470.4312-0.0454-0.0216-0.77130.15640.03420.33730.0763-0.05560.3203-0.10750.306227.813416.2581-8.3819
102.78110.5492-2.0473.3408-2.33133.1917-0.09460.33240.6839-0.54990.35681.1257-0.8103-1.1053-0.1350.43430.0449-0.07870.44090.07090.484113.998811.9646-25.6596
114.17530.95790.05073.02330.21883.3802-0.0074-0.07770.37650.21370.0312-0.0041-0.20990.01290.02780.26050.03850.00260.1452-0.0180.308223.050213.502-17.1499
126.55092.3761.78585.37652.41896.7159-0.23150.73910.8242-0.5359-0.0344-0.4175-0.78170.23840.06560.2976-0.0308-0.01220.2640.09820.430933.93418.1241-27.7245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 212 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 18 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 34 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 72 )
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 90 )
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 127 )
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 147 )
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 161 )
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 191 )
12X-RAY DIFFRACTION12chain 'B' and (resid 192 through 212 )

+
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