[English] 日本語
Yorodumi
- PDB-2abb: Structure of PETN reductase Y186F in complex with cyanide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2abb
TitleStructure of PETN reductase Y186F in complex with cyanide
Componentspentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / PETN reductase / proton transfer / flavoenzyme
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / ISOPROPYL ALCOHOL / THIOCYANATE ION / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKhan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S.
CitationJournal: Febs J. / Year: 2005
Title: Proton transfer in the oxidative half-reaction of pentaerythritol tetranitrate reductase
Authors: Khan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 1.4Nov 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 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9634
Polymers39,3881
Non-polymers5753
Water11,818656
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.618, 68.664, 88.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein pentaerythritol tetranitrate reductase / PETN reductase


Mass: 39388.000 Da / Num. of mol.: 1 / Mutation: Y186F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71278, EC: 1.7.99.-
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25%(w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid(pH 6.2), 17%(v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→15 Å / Num. all: 172733 / Num. obs: 169624 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 1→1.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.489 / % possible all: 84

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYR

1vyr


Resolution: 1→14.37 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.696 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15486 8938 5 %RANDOM
Rwork0.1384 ---
all0.13924 172733 --
obs0.13924 169624 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.713 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.82 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1→14.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 38 656 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212910
X-RAY DIFFRACTIONr_bond_other_d0.0030.022666
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9673981
X-RAY DIFFRACTIONr_angle_other_deg1.236188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70523.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1151525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
X-RAY DIFFRACTIONr_nbd_refined0.2540.2641
X-RAY DIFFRACTIONr_nbd_other0.2590.23305
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2520
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4760.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.289
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.51828
X-RAY DIFFRACTIONr_mcbond_other0.4961.5747
X-RAY DIFFRACTIONr_mcangle_it1.50122942
X-RAY DIFFRACTIONr_scbond_it1.88231099
X-RAY DIFFRACTIONr_scangle_it2.7524.51033
X-RAY DIFFRACTIONr_rigid_bond_restr0.93435602
X-RAY DIFFRACTIONr_sphericity_free4.3923656
X-RAY DIFFRACTIONr_sphericity_bonded2.87835508
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 539
Rwork0.337 10677

+
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