[English] 日本語
Yorodumi
- PDB-4rnx: K154 Circular Permutation of Old Yellow Enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rnx
TitleK154 Circular Permutation of Old Yellow Enzyme
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CIRCULAR PERMUTATION / CATALYSIS / OLD YELLOW ENZYME / FLAVIN COFACTOR
Function / homology
Function and homology information


NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsHorton, J.R. / Daugherty, A.B. / Cheng, X. / Lutz, S.
CitationJournal: ACS Catal / Year: 2015
Title: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME.
Authors: Daugherty, A.B. / Horton, J.R. / Cheng, X. / Lutz, S.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / 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 / _entity.formula_weight / _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: NADPH dehydrogenase 1
B: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,17210
Polymers89,8872
Non-polymers1,2858
Water20,1951121
1
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6486
Polymers44,9431
Non-polymers7055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5244
Polymers44,9431
Non-polymers5803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.087, 57.982, 85.900
Angle α, β, γ (deg.)102.46, 98.36, 111.19
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 44943.445 Da / Num. of mol.: 2 / Fragment: UNP residues 154-397, 2-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q02899, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG 2KMME, 0.1M Potassium Thiocyanate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→27.11 Å / Num. all: 207000 / Num. obs: 196866 / % possible obs: 95.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.9 / Num. unique all: 19029 / % possible all: 92

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OYA

1oya


Resolution: 1.25→27.11 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 2001 1.02 %RANDOM
Rwork0.1338 ---
obs0.1341 196804 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6191 0 86 1121 7398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036519
X-RAY DIFFRACTIONf_angle_d0.9468866
X-RAY DIFFRACTIONf_dihedral_angle_d13.2112387
X-RAY DIFFRACTIONf_chiral_restr0.075924
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28160.25821340.212812943X-RAY DIFFRACTION88
1.2816-1.31630.21811300.187613491X-RAY DIFFRACTION92
1.3163-1.3550.21751500.174813599X-RAY DIFFRACTION93
1.355-1.39880.2081430.163313707X-RAY DIFFRACTION93
1.3988-1.44880.19231460.146213724X-RAY DIFFRACTION94
1.4488-1.50680.1941380.132213826X-RAY DIFFRACTION94
1.5068-1.57530.15061430.118313892X-RAY DIFFRACTION95
1.5753-1.65840.14981400.113313963X-RAY DIFFRACTION95
1.6584-1.76220.13941430.114114074X-RAY DIFFRACTION96
1.7622-1.89830.17641420.121214107X-RAY DIFFRACTION96
1.8983-2.08920.14751480.126214224X-RAY DIFFRACTION97
2.0892-2.39140.15071470.127814280X-RAY DIFFRACTION97
2.3914-3.01230.15391480.140114424X-RAY DIFFRACTION98
3.0123-27.11010.1491490.128614549X-RAY DIFFRACTION99

+
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://pdbjlvh1.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