[English] 日本語
Yorodumi
- PDB-3gx9: Structure of morphinone reductase N189A mutant in complex with te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gx9
TitleStructure of morphinone reductase N189A mutant in complex with tetrahydroNAD
ComponentsMorphinone reductase
KeywordsOXIDOREDUCTASE / H-tunnelling / flavoprotein / NADH / morphinone reductase / hydride transfer
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 / Chem-TXD / Morphinone reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLafite, P. / Scrutton, N.S. / Leys, D.
CitationJournal: Chembiochem / Year: 2009
Title: Parallel Pathways and Free-Energy Landscapes for Enzymatic Hydride Transfer Probed by Hydrostatic Pressure
Authors: Pudney, C.R. / McGrory, T. / Lafite, P. / Pang, J. / Hay, S. / Leys, D. / Sutcliffe, M.J. / Scrutton, N.S.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: 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 1.3Nov 1, 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: Morphinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3723
Polymers41,2481
Non-polymers1,1242
Water3,135174
1
A: Morphinone reductase
hetero molecules

A: Morphinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7436
Polymers82,4962
Non-polymers2,2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area6150 Å2
ΔGint-24 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.651, 122.941, 179.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

-
Components

#1: Protein Morphinone reductase


Mass: 41247.867 Da / Num. of mol.: 1 / Mutation: N189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: M10 / Gene: morB / Plasmid: pMORB2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q51990
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-TXD / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, pH7.5, 0.1M MgCl2, 35% PEG400, Crystals were soaked in a 50% Ammonium sulfate Solution, containing 100mM NADH4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9696 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9696 Å / Relative weight: 1
ReflectionResolution: 2.28→44.9 Å / Num. obs: 23517 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.4
Reflection shellResolution: 2.28→2.5 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.5 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R14

2r14


Resolution: 2.28→44.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.289 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22935 1188 5.1 %RANDOM
Rwork0.1831 ---
obs0.18545 22214 91.29 %-
all-25634 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.28→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 57 174 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222952
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9864034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0223.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1331526
X-RAY DIFFRACTIONr_chiral_restr0.1140.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212350
X-RAY DIFFRACTIONr_mcbond_it0.8771.51844
X-RAY DIFFRACTIONr_mcangle_it1.54322936
X-RAY DIFFRACTIONr_scbond_it2.5731108
X-RAY DIFFRACTIONr_scangle_it3.7994.51098
LS refinement shellResolution: 2.279→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 67 -
Rwork0.331 1551 -
obs--88.22 %

+
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