[English] 日本語
Yorodumi
- PDB-6qkx: 2-Naphthoyl-CoA Reductase-DiHydroNaphthoyl-CoA complex(NCR-DHNCoA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qkx
Title2-Naphthoyl-CoA Reductase-DiHydroNaphthoyl-CoA complex(NCR-DHNCoA co-crystallized complex)
ComponentsNCR
KeywordsFLAVOPROTEIN / Reductase / 2-Naphthoyl-CoA / 2-Naphthoyl-CoA reductase / Naphthalene / FAD / FMN / [4Fe-4S] / Hydride transfer / Co-crystallized
Function / homology
Function and homology information


FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
: / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Chem-J5H / IRON/SULFUR CLUSTER / NADH oxidase
Similarity search - Component
Biological speciesbacterium enrichment culture clone N47 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKayastha, K. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 1976, SPP 1927 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors.
Authors: Willistein, M. / Bechtel, D.F. / Muller, C.S. / Demmer, U. / Heimann, L. / Kayastha, K. / Schunemann, V. / Pierik, A.J. / Ullmann, G.M. / Ermler, U. / Boll, M.
History
DepositionJan 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4365
Polymers77,9201
Non-polymers2,5154
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-36 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.860, 176.860, 49.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NCR


Mass: 77920.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF4, FAD, FMN, LIG
Source: (gene. exp.) bacterium enrichment culture clone N47 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: E1YD54

-
Non-polymers , 5 types, 31 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-J5H / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] naphthalene-2-carbothioate


Mass: 921.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N7O17P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 3350, NaF

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29947 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rsym value: 0.071 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2975 / CC1/2: 0.895 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qkr

6qkr


Resolution: 2.4→47.418 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 1449 4.84 %
Rwork0.2291 --
obs0.2313 29947 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 152 27 5243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045317
X-RAY DIFFRACTIONf_angle_d0.9157212
X-RAY DIFFRACTIONf_dihedral_angle_d9.0643158
X-RAY DIFFRACTIONf_chiral_restr0.052789
X-RAY DIFFRACTIONf_plane_restr0.0071567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48570.43571480.35212830X-RAY DIFFRACTION100
2.4857-2.58520.43371380.33472865X-RAY DIFFRACTION100
2.5852-2.70290.44851370.37022804X-RAY DIFFRACTION98
2.7029-2.84540.38191380.30612832X-RAY DIFFRACTION100
2.8454-3.02360.35131350.27222850X-RAY DIFFRACTION99
3.0236-3.2570.33241500.25932817X-RAY DIFFRACTION99
3.257-3.58470.29251380.25412846X-RAY DIFFRACTION99
3.5847-4.10320.25711310.21642850X-RAY DIFFRACTION98
4.1032-5.16850.23111640.18522850X-RAY DIFFRACTION100
5.1685-47.42720.22841700.19412955X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.3383 Å / Origin y: -27.9047 Å / Origin z: -9.1934 Å
111213212223313233
T0.8007 Å20.0237 Å2-0.0437 Å2-0.7818 Å20.1064 Å2--0.7734 Å2
L1.5759 °2-0.8995 °20.3289 °2-1.6907 °2-0.1898 °2--0.5992 °2
S-0.0275 Å °-0.0543 Å °0.032 Å °-0.0994 Å °0.1308 Å °1.0052 Å °-0.0166 Å °-0.2571 Å °-0.0859 Å °
Refinement TLS groupSelection details: all

+
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