[English] 日本語
Yorodumi
- PDB-5jro: The crystal structure of azoreductase from Yersinia pestis CO92 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jro
TitleThe crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) 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
FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of azoreductase from Yersinia pestis CO92 in its Apo form
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9644
Polymers43,7802
Non-polymers1842
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-20 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.257, 45.135, 72.699
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 21890.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: azoR, YPO2323, y2010, YP_2110 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q8ZE60, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES:NaOH, 30% (w/v) PEG 3000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2014 / Details: Mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.54→33.5 Å / Num. obs: 12240 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.74
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.35 / % possible all: 81.3

-
Processing

Software
NameVersionClassification
PHENIX(dev-2386_1692: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 4ESE

4ese


Resolution: 2.54→33.5 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 529 4.85 %random
Rwork0.1997 ---
obs0.202 10911 86.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 12 20 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032804
X-RAY DIFFRACTIONf_angle_d0.5113811
X-RAY DIFFRACTIONf_dihedral_angle_d15.1941685
X-RAY DIFFRACTIONf_chiral_restr0.041468
X-RAY DIFFRACTIONf_plane_restr0.004486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.7850.31971030.27611813X-RAY DIFFRACTION62
2.785-3.18770.29041140.24982532X-RAY DIFFRACTION85
3.1877-4.01510.28011520.19792987X-RAY DIFFRACTION100
4.0151-33.50.20041600.16773050X-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)
19.72170.6865-5.47325.3769-1.57228.9143-0.6360.4646-1.0007-0.63420.2661-0.93230.8179-0.76090.3890.4225-0.019-0.0540.2743-0.09610.374433.4312-35.5325-16.8249
23.09641.16070.29984.03072.29053.2533-0.108-0.0965-0.35-0.0135-0.1642-0.41150.3989-0.38620.43331.03670.0439-0.04140.2198-0.1750.539634.7872-42.3407-20.6694
32.2621-1.1895-0.52654.7483.72423.0637-0.12760.1142-0.1651-0.60270.4585-0.8290.10940.5933-0.19670.52130.16190.18440.4213-0.0240.482141.8183-35.9413-18.327
43.80290.2816-1.48113.65070.36293.4419-0.0342-0.53720.53360.28290.3856-0.73860.01510.24580.09420.1336-0.0820.04550.4087-0.07650.222328.4035-24.1563-7.4328
57.0404-2.45994.982.375-1.97653.8076-0.2546-0.12462.2093-0.5414-0.1223-0.5545-2.22941.05190.37720.6285-0.13410.16340.4229-0.04190.73632.1732-7.8483-6.4721
61.9697-0.03540.28241.35610.46211.28530.2576-0.2357-0.1294-0.34240.1325-0.1947-0.12920.1873-0.22120.173-0.03830.12280.3034-0.05690.137131.0617-23.3423-14.5509
73.0771-0.53452.11880.1450.05784.9458-0.07550.36870.2858-1.23170.0354-0.6132-1.06850.2787-0.06310.655-0.08540.19410.3751-0.00380.30335.9481-11.8965-26.2932
81.2328-1.5201-1.41014.3311-0.21073.18180.16930.5282-0.5944-0.2393-0.15570.60490.1037-0.9390.56760.6269-0.07820.04520.6018-0.15990.316722.1168-32.1799-27.2439
95.121-1.07370.51614.99190.69644.7232-0.03220.4507-0.6077-1.04010.05010.29930.3783-0.18140.03850.5433-0.0323-0.00510.292-0.00110.234126.9146-27.3561-27.584
107.5702-1.16824.43259.005-0.12978.7116-0.47850.8502-0.5045-0.7192-0.16680.76150.00920.13130.55510.86460.0420.08980.4003-0.13660.403931.6293-43.5733-29.7787
117.5798-3.43581.40814.1873-0.84312.9355-0.06180.0810.44790.092-0.05270.5524-0.6120.11430.11620.3083-0.014-0.03920.21040.00190.33366.291-9.4488-7.9362
123.9478-0.4086-1.81232.5955-0.99343.56370.1625-0.2418-0.16410.08210.01340.4323-0.07270.035-0.08980.1457-0.0929-0.08350.1836-0.05860.195510.4913-25.2835-6.2798
131.6271-0.66350.32363.9922-0.20212.5255-0.04150.20980.204-0.65470.01830.1783-0.1177-0.0209-0.00290.3109-0.0303-0.13010.23840.03520.31995.7741-19.4813-18.473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 112 )
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 189 )
10X-RAY DIFFRACTION10chain 'A' and (resid 190 through 201 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 52 )
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 102 )
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 201 )

+
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