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

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Basic information

Entry
Database: PDB / ID: 6gas
TitleCrystal structure of oxidised ferredoxin/flavodoxin NADP+ oxidoreductase 2 (FNR2) 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
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGudim, I. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway231669 Norway
CitationJournal: 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.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)150,40712
Polymers147,1724
Non-polymers3,2348
Water3,783210
1
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2036
Polymers73,5862
Non-polymers1,6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-64 kcal/mol
Surface area28860 Å2
MethodPISA
2
C: Ferredoxin--NADP reductase
D: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2036
Polymers73,5862
Non-polymers1,6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-70 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.660, 109.660, 242.519
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPHEPHEchain 'A'AA6 - 3316 - 331
12FADFADFADFADchain 'A'AE1001
23ASNASNPHEPHE(chain 'B' and (resid 6 through 331 or resid 1001))BB6 - 3316 - 331
24FADFADFADFAD(chain 'B' and (resid 6 through 331 or resid 1001))BG1001
35ASNASNPHEPHE(chain 'C' and (resid 6 through 331 or resid 1001))CC6 - 3316 - 331
36FADFADFADFAD(chain 'C' and (resid 6 through 331 or resid 1001))CI1001
47ASNASNPHEPHEchain 'D'DD6 - 3316 - 331
48FADFADFADFADchain 'D'DK1001

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Components

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


Mass: 36793.109 Da / Num. of mol.: 4
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)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_4926 / Production host: Escherichia coli (E. coli) / References: UniProt: Q816D9, ferredoxin-NADP+ reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.02 M Tris pH 7.0, 7.7 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.4→48.5 Å / Num. obs: 66924 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 50.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.145 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 2 / Num. unique obs: 4445 / CC1/2: 0.749 / Rrim(I) all: 1.076 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZW

3lzw


Resolution: 2.4→46.6 Å / SU ML: 0.3814 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7846
RfactorNum. reflection% reflection
Rfree0.2621 3385 5.06 %
Rwork0.2074 --
obs0.2101 66847 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10206 0 216 210 10632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011110642
X-RAY DIFFRACTIONf_angle_d1.255614432
X-RAY DIFFRACTIONf_chiral_restr0.07061598
X-RAY DIFFRACTIONf_plane_restr0.00811832
X-RAY DIFFRACTIONf_dihedral_angle_d16.62576300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.39781750.33012581X-RAY DIFFRACTION100
2.43-2.470.36371520.29392578X-RAY DIFFRACTION100
2.47-2.510.36861350.27692606X-RAY DIFFRACTION100
2.51-2.550.32111640.26072633X-RAY DIFFRACTION100
2.55-2.590.31741270.26842590X-RAY DIFFRACTION100
2.59-2.640.31641280.27412627X-RAY DIFFRACTION99.96
2.64-2.690.34051500.26722595X-RAY DIFFRACTION100
2.69-2.750.3541350.25582655X-RAY DIFFRACTION100
2.75-2.810.31581460.25672599X-RAY DIFFRACTION100
2.81-2.870.36591060.25072645X-RAY DIFFRACTION100
2.87-2.940.27241110.24382637X-RAY DIFFRACTION99.96
2.94-3.020.29361780.23582616X-RAY DIFFRACTION100
3.02-3.110.29791540.22992608X-RAY DIFFRACTION100
3.11-3.210.30521480.23772613X-RAY DIFFRACTION100
3.21-3.330.30651030.23632673X-RAY DIFFRACTION100
3.33-3.460.32351300.2342646X-RAY DIFFRACTION100
3.46-3.620.23791280.22812649X-RAY DIFFRACTION100
3.62-3.810.28431380.22032659X-RAY DIFFRACTION100
3.81-4.050.26181770.20972621X-RAY DIFFRACTION100
4.05-4.360.23911220.18542678X-RAY DIFFRACTION99.61
4.36-4.80.2281280.16812673X-RAY DIFFRACTION99.57
4.8-5.490.23951470.16392702X-RAY DIFFRACTION100
5.49-6.920.20591490.17482723X-RAY DIFFRACTION100
6.92-46.610.16611540.14632855X-RAY DIFFRACTION99.54

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