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- PDB-6gar: Crystal structure of oxidised ferredoxin/flavodoxin NADP+ oxidore... -

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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 / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / NADP binding / flavin adenine dinucleotide 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-FAD / 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


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


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


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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