[English] 日本語
Yorodumi
- PDB-3r5y: Structure of a Deazaflavin-dependent nitroreductase from Nocardia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r5y
TitleStructure of a Deazaflavin-dependent nitroreductase from Nocardia farcinica, with co-factor F420
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / PA-824 / nitroimidazoles / split barrel-like fold / DUF385 / deazaflavin-dependent nitroreductase / F420
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
COENZYME F420 / Uncharacterized protein
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å
AuthorsCellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, A. / Lee, Y.S. ...Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I.M. / Choi, I. / Nayya, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H.
CitationJournal: Structure / Year: 2012
Title: Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.
Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. ...Authors: Cellitti, S.E. / Shaffer, J. / Jones, D.H. / Mukherjee, T. / Gurumurthy, M. / Bursulaya, B. / Boshoff, H.I. / Choi, I. / Nayyar, A. / Lee, Y.S. / Cherian, J. / Niyomrattanakit, P. / Dick, T. / Manjunatha, U.H. / Barry, C.E. / Spraggon, G. / Geierstanger, B.H.
History
DepositionMar 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4248
Polymers65,3294
Non-polymers3,0944
Water8,755486
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,3321
Non-polymers7741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,3321
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,3321
Non-polymers7741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1062
Polymers16,3321
Non-polymers7741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.956, 71.956, 115.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Putative uncharacterized protein


Mass: 16332.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (bacteria) / Gene: NFA_33440 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: UniProt: Q5YUF0
#2: Chemical
ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 40% MPD, 0.1M sodium acetate trihydrate with equimolar protein and co-factor, pH 5.0, vapor diffusion, sitting drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54170 / Num. obs: 54170 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.088 / Χ2: 1.606 / Net I/σ(I): 28.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.865.40.6651.94453820.622100
1.86-1.945.40.4923.16754310.855100
1.94-2.035.40.3075.05653880.795100
2.03-2.135.40.2397.05353921.003100
2.13-2.275.40.18310.21154201.19100
2.27-2.445.40.13415.22253861.284100
2.44-2.695.40.1152054091.64100
2.69-3.085.30.09730.04354262.557100
3.08-3.885.10.07144.6154453.351100
3.88-505.30.05454.50854912.90699.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.35 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.03 Å
Translation2.5 Å45.03 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3R5P

3r5p


Resolution: 1.801→45.031 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.18 / σ(F): 0.21 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2591 5.07 %random
Rwork0.1731 ---
obs0.1751 51143 94.37 %-
all-51169 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.704 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 118.14 Å2 / Biso mean: 29.3676 Å2 / Biso min: 13.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.9218 Å20 Å2-0 Å2
2--0.9218 Å20 Å2
3----1.8436 Å2
Refinement stepCycle: LAST / Resolution: 1.801→45.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 212 486 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084771
X-RAY DIFFRACTIONf_angle_d1.1316532
X-RAY DIFFRACTIONf_chiral_restr0.077684
X-RAY DIFFRACTIONf_plane_restr0.006853
X-RAY DIFFRACTIONf_dihedral_angle_d18.9881728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.801-1.86570.27682440.218242714515451584
1.8657-1.94040.24242390.204544174656465686
1.9404-2.02870.21982430.174647524995499593
2.0287-2.13560.22812850.176448135098509894
2.1356-2.26940.22052830.173348635146514695
2.2694-2.44460.21572410.172649535194519496
2.4446-2.69060.22392580.176250595317531798
2.6906-3.07990.22042680.178150895357535799
3.0799-3.880.19982580.159515554135413100
3.88-45.04530.19762720.166751805452545299
Refinement TLS params.Method: refined / Origin x: 1.8948 Å / Origin y: 34.3209 Å / Origin z: -6.6308 Å
111213212223313233
T0.1332 Å2-0.0096 Å20.0093 Å2-0.1472 Å2-0.0118 Å2--0.1508 Å2
L0.0903 °2-0.0297 °20.0957 °2-0.0271 °2-0.045 °2--0.1104 °2
S-0.0205 Å °-0.0102 Å °-0.0341 Å °0.0093 Å °-0.001 Å °-0.0058 Å °-0.0005 Å °0.033 Å °0.0154 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 146
2X-RAY DIFFRACTION1allB6 - 146
3X-RAY DIFFRACTION1allC6 - 146
4X-RAY DIFFRACTION1allD5 - 146
5X-RAY DIFFRACTION1allA1 - 147
6X-RAY DIFFRACTION1allB1 - 147
7X-RAY DIFFRACTION1allC1 - 147
8X-RAY DIFFRACTION1allD1 - 147
9X-RAY DIFFRACTION1allB1 - 485
10X-RAY DIFFRACTION1allC1 - 148

+
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://pdbjlc1.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