[English] 日本語
Yorodumi
- PDB-2reh: Mechanistic and Structural Analyses of the Roles of Arg409 and As... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2reh
TitleMechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase
ComponentsNitroalkane oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / NITROALKANEFAD / FLAVOPROTEIN
Function / homology
Function and homology information


nitroalkane oxidase / nitroalkane oxidase activity / butyrate catabolic process / detoxification / oxidoreductase activity, acting on the CH-CH group of donors / fatty acid beta-oxidation using acyl-CoA dehydrogenase / FAD binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Nitroalkane oxidase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M.
Citation
Journal: Biochemistry / Year: 2007
Title: Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.
Authors: Fitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M.
#1: Journal: Biochemistry / Year: 2006
Title: Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover
Authors: Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Oct 25, 2023Group: 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.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitroalkane oxidase
B: Nitroalkane oxidase
C: Nitroalkane oxidase
D: Nitroalkane oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0758
Polymers192,9334
Non-polymers3,1424
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26010 Å2
ΔGint-154 kcal/mol
Surface area54230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.934, 108.934, 337.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 2 - 431 / Label seq-ID: 2 - 431

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Nitroalkane oxidase


Mass: 48233.273 Da / Num. of mol.: 4 / Mutation: D402E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PETNAO4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X1D8, nitroalkane oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24-26% PEG 3350, 30% glycerol, 0.1M Na Cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 81048 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.081 / Net I/σ(I): 22.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.27 / Num. unique all: 4878 / Rsym value: 0.414 / % possible all: 53.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c0u

2c0u


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.867 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 4051 5 %RANDOM
Rwork0.20364 ---
obs0.20657 76997 88.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.049 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13204 0 212 56 13472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02213712
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.98518651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09751716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33724.442547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1152322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3341572
X-RAY DIFFRACTIONr_chiral_restr0.1370.22120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210164
X-RAY DIFFRACTIONr_nbd_refined0.2260.26319
X-RAY DIFFRACTIONr_nbtor_refined0.3080.29194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2403
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.228
X-RAY DIFFRACTIONr_mcbond_it1.0071.58858
X-RAY DIFFRACTIONr_mcangle_it1.565213807
X-RAY DIFFRACTIONr_scbond_it2.51835861
X-RAY DIFFRACTIONr_scangle_it3.8714.54844
Refine LS restraints NCS

Ens-ID: 1 / Number: 3293 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.280.5
2Bmedium positional0.340.5
3Cmedium positional0.330.5
4Dmedium positional0.270.5
1Amedium thermal1.142
2Bmedium thermal1.832
3Cmedium thermal1.322
4Dmedium thermal1.512
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 183 -
Rwork0.29 3232 -
obs--50.95 %

+
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