[English] 日本語
Yorodumi
- PDB-5h5j: Complex between ferredoxin and ferredoxin-NADP+ reductase from ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h5j
TitleComplex between ferredoxin and ferredoxin-NADP+ reductase from maize root
Components
  • Ferredoxin--NADP reductase
  • Ferredoxin-3, chloroplastic
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Electron transfer complex / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


etioplast stroma / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / NADPH binding / photosynthesis / chloroplast ...etioplast stroma / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / chloroplast stroma / NADPH binding / photosynthesis / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Ferredoxin [2Fe-2S], plant / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / Ferredoxin [2Fe-2S], plant / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Flavoprotein pyridine nucleotide cytochrome reductase / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin--NADP reductase, chloroplastic / Ferredoxin-3, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKurisu, G. / Hase, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST-CREST Japan
Citation
Journal: Photosyn. Res. / Year: 2017
Title: Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP(+) oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation
Authors: Shinohara, F. / Kurisu, G. / Hanke, G. / Bowsher, C. / Hase, T. / Kimata-Ariga, Y.
#1: Journal: Photosyn. Res. / Year: 2004
Title: Fd : FNR Electron Transfer Complexes: Evolutionary Refinement of Structural Interactions
Authors: Hanke, G.T. / Kurisu, G. / Kusunoki, M. / Hase, T.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin-3, chloroplastic
C: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3746
Polymers79,6273
Non-polymers1,7473
Water6,017334
1
A: Ferredoxin--NADP reductase
B: Ferredoxin-3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9564
Polymers44,9942
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-27 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4182
Polymers34,6321
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.718, 126.576, 59.367
Angle α, β, γ (deg.)90.00, 114.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ferredoxin--NADP reductase


Mass: 34632.242 Da / Num. of mol.: 2 / Fragment: UNP residues 19-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase
#2: Protein Ferredoxin-3, chloroplastic / Ferredoxin III / Fd III


Mass: 10362.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: FDX3, PFD3 / Production host: Escherichia coli (E. coli) / References: UniProt: P27788
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20 % PEG6000, 100 mM Sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 91157 / % possible obs: 99.4 % / Redundancy: 3.74 % / Biso Wilson estimate: 19.9 Å2 / Net I/σ(I): 25.7

-
Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H59

5h59


Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4560843.87 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USE
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1217 5 %RANDOM
Rwork0.191 ---
obs0.191 24282 99.4 %-
Solvent computationBsol: 35.577 Å2 / ksol: 0.370307 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å23.08 Å2
2--4.78 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: 1 / Resolution: 2.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 110 334 6043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 199 5 %
Rwork0.231 3781 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fad.parfad.top
X-RAY DIFFRACTION4fes.parfes.top

+
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