[English] 日本語
Yorodumi
- PDB-3h96: Msmeg_3358 F420 Reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h96
TitleMsmeg_3358 F420 Reductase
ComponentsF420-H2 Dependent Reductase A
KeywordsFLAVOPROTEIN / PNPOX / F420 / Flavin / Reductase / Aflatoxin
Function / homology
Function and homology information


coenzyme F420 binding / oxidoreductase activity / plasma membrane
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
Deazaflavin-dependent nitroreductase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJackson, C.J. / French, N. / Newman, J. / Taylor, M.C. / Russell, R.J. / Oakeshott, J.G.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Identification and characterization of two families of F420 H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation.
Authors: Taylor, M.C. / Jackson, C.J. / Tattersall, D.B. / French, N. / Peat, T.S. / Newman, J. / Briggs, L.J. / Lapalikar, G.V. / Campbell, P.M. / Scott, C. / Russell, R.J. / Oakeshott, J.G.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F420-H2 Dependent Reductase A
B: F420-H2 Dependent Reductase A
C: F420-H2 Dependent Reductase A
D: F420-H2 Dependent Reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6255
Polymers62,5634
Non-polymers621
Water6,269348
1
A: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F420-H2 Dependent Reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7032
Polymers15,6411
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 71.150, 63.840
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
F420-H2 Dependent Reductase A


Mass: 15640.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: MC2 / Gene: MSMEG_3356 / Plasmid: pDEST 17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: A0QXM5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 36 w/v polyethylene glycol monomethyl ether 5000, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979461 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: double crystal monochromator with sagitally bent second crystal horizontal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979461 Å / Relative weight: 1
ReflectionResolution: 2→47.51 Å / Num. obs: 34129 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.2 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→45.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.917 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25508 2674 8 %RANDOM
Rwork0.18451 ---
obs0.18939 30897 92.6 %-
all-30897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-1.57 Å2
2---0.46 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 4 348 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9386021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48223.116199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9091536
X-RAY DIFFRACTIONr_chiral_restr0.1310.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213454
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4691.52774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37324479
X-RAY DIFFRACTIONr_scbond_it3.08631629
X-RAY DIFFRACTIONr_scangle_it4.7834.51532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 654 -
Rwork0.189 1146 -
obs--67.57 %
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)
10.31550.09920.24910.28340.00120.2205-0.0027-0.0212-0.0003-0.033-0.003-0.01510.0043-0.01590.00570.0271-0.00270.00680.0280.00350.01251.9535.5531.277
20.49620.1765-0.09280.33920.11180.09350.01250.0292-0.00990.0193-0.0091-0.00780.0046-0.0106-0.00350.02350.00440.00620.0396-0.00270.0056-7.7047.029-30.672
30.2481-0.11950.04370.50990.05660.0220.0020.01540.02340.0129-0.0103-0.01290.0067-0.00070.00830.0261-0.00410.01120.02690.00080.015522.1165.688-41.1
40.6573-0.2146-0.19770.3986-0.03060.08840.0286-0.0207-0.0007-0.0274-0.0260.0016-0.00440.0065-0.00260.0160.00030.00750.0518-0.00280.004431.856.928-9.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 142
2X-RAY DIFFRACTION2B6 - 142
3X-RAY DIFFRACTION3C6 - 142
4X-RAY DIFFRACTION4D6 - 142

+
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