[English] 日本語
Yorodumi
- PDB-6gar: Crystal structure of oxidised ferredoxin/flavodoxin NADP+ oxidore... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gar
TitleCrystal structure of oxidised ferredoxin/flavodoxin NADP+ oxidoreductase 1 (FNR1) from Bacillus cereus
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / ferredoxin/flavodoxin reductase / electron transfer / FAD / flavoprotein
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Ferredoxin--NADP reductase, type 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / OXAMIC ACID / L(+)-TARTARIC ACID / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSkramo, S. / Gudim, I. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway231669 Norway
Citation
Journal: Biochemistry / Year: 2018
Title: The Characterization of Different Flavodoxin Reductase-Flavodoxin (FNR-Fld) Interactions Reveals an Efficient FNR-Fld Redox Pair and Identifies a Novel FNR Subclass.
Authors: Gudim, I. / Hammerstad, M. / Lofstad, M. / Hersleth, H.P.
#1: Journal: Acta Cryst. F / Year: 2014
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus
Authors: Skramo, S. / Hersleth, H.-P. / Hammerstad, M. / Andersson, K.K. / Rohr, A.K.
History
DepositionApr 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4048
Polymers77,4462
Non-polymers1,9586
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-53 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.166, 164.330, 95.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin--NADP reductase / Fd-NADP(+) reductase


Mass: 38722.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Gene: BC_0385 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81IK1, ferredoxin-NADP+ reductase

-
Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate, 20 mM sodium potassium tartrate, 20 mM sodium oxamate, 50 mM HEPES, 50 mM MOPS pH 7.5, 12.5%(v/v) MPD, 12.5%(w/v) PEG 1K, 12.5%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→54.78 Å / Num. obs: 35326 / % possible obs: 98.5 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.148 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3361 / CC1/2: 0.629 / Rrim(I) all: 0.748 / % possible all: 90.6

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZX

3lzx


Resolution: 2.4→48.983 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2349 1709 4.84 %
Rwork0.186 --
obs0.1884 35276 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 132 176 5677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085605
X-RAY DIFFRACTIONf_angle_d1.0057588
X-RAY DIFFRACTIONf_dihedral_angle_d16.7663283
X-RAY DIFFRACTIONf_chiral_restr0.058847
X-RAY DIFFRACTIONf_plane_restr0.006966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.32941260.26122509X-RAY DIFFRACTION89
2.4706-2.55040.28721270.2462661X-RAY DIFFRACTION96
2.5504-2.64150.26581480.22342830X-RAY DIFFRACTION100
2.6415-2.74730.28131620.22262745X-RAY DIFFRACTION100
2.7473-2.87230.24561350.21112823X-RAY DIFFRACTION100
2.8723-3.02370.26861430.20522767X-RAY DIFFRACTION99
3.0237-3.21310.24361450.19472816X-RAY DIFFRACTION100
3.2131-3.46110.22511400.19212839X-RAY DIFFRACTION100
3.4611-3.80930.21431600.16742836X-RAY DIFFRACTION99
3.8093-4.36030.20511500.15442828X-RAY DIFFRACTION100
4.3603-5.49230.20571420.15462876X-RAY DIFFRACTION99
5.4923-48.99350.22481310.17513037X-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://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