[English] 日本語
Yorodumi
- PDB-1bqe: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY (T155G) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bqe
TitleFERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY (T155G)
ComponentsFERREDOXIN--NADP REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / NADP REDUCTASE
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / 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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHermoso, J.A. / Mayoral, T. / Medina, M. / Martinez-Ripoll, M. / Martinez-Julvez, M. / Sanz-Aparicio, J. / Gomez-Moreno, C.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Probing the determinants of coenzyme specificity in ferredoxin-NADP+ reductase by site-directed mutagenesis.
Authors: Medina, M. / Luquita, A. / Tejero, J. / Hermoso, J. / Mayoral, T. / Sanz-Aparicio, J. / Grever, K. / Gomez-Moreno, C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: X-Ray Structure of the Ferredoxin:Nadp+ Reductase from the Cyanobacterium Anabaena Pcc 7119 at 1.8 A Resolution, and Crystallographic Studies of Nadp+ Binding at 2.25 A Resolution
Authors: Serre, L. / Vellieux, F.M. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M.
History
DepositionAug 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Nov 3, 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 1.5Aug 9, 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: FERREDOXIN--NADP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0403
Polymers33,1591
Non-polymers8822
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.130, 88.130, 97.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein FERREDOXIN--NADP REDUCTASE / FNR


Mass: 33158.656 Da / Num. of mol.: 1 / Mutation: T155G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Production host: Escherichia coli (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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 Å3/Da / Density % sol: 60 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125.9 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
35 %(w/v)beta-octylglucoside1drop
418 %(w/v)PEG60001reservoir
520 mMammonium sulfate1reservoir
60.1 Msodium acetate1reservoirpH5.0

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→40.13 Å / Num. obs: 15728 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 6.3
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.27 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40.1 Å / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 97.2 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUE

1que


Resolution: 2.45→9 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE-R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1074 7 %RANDOM
Rwork0.16 ---
obs0.16 15377 99.67 %-
Displacement parametersBiso mean: 19.84 Å2
Refinement stepCycle: LAST / Resolution: 2.45→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 58 267 2660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 -12.5 %
Rwork0.21 875 -
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.4
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.3 / % reflection Rfree: 12.5 % / Rfactor Rwork: 0.21

+
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