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- PDB-3lo8: Crystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reduct... -

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Basic information

Entry
Database: PDB / ID: 3lo8
TitleCrystal Structure of The Oxidized Form of Ferredoxin:NADP+ Reductase From Maize Root at 1.05 Angstroms
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / FAD / Flavoprotein / NADP
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / NADPH binding / photosynthesis / electron transport chain / electron transfer activity
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / 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--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / 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 speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsFaber, H.R. / Karplus, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
Authors: Tronrud, D.E. / Berkholz, D.S. / Karplus, P.A.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6573
Polymers34,8481
Non-polymers8092
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.140, 59.140, 186.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is the contents of the asymmetric unit

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 34848.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: Q41736, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7154.53
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6Peg 8000, Na Cacodylate, Mg Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop6Peg 8000, Na Cacodylate, Mg Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 14-BM-C21
SYNCHROTRONAPS 1-BM-C31
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCD1999
ADSC QUANTUM 42CCD1999
ADSC QUANTUM 43CCD2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 177114 / Num. obs: 177114 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 57
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8768 / % possible all: 99.5

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Processing

Software
NameClassification
SHELXL-97refinement
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1jb9

1jb9


Resolution: 1.05→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Shelxl Conjugate Gradient Least Squares
RfactorNum. reflection% reflectionSelection details
Rfree0.1554 16388 -random
Rwork0.125 ---
all0.125 176906 --
obs0.125 176906 99.7 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 54 644 3082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.208
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_from_restr_planes0.366
X-RAY DIFFRACTIONs_approx_iso_adps0.102
LS refinement shellResolution: 1.05→1.16 Å /
Num. reflection% reflection
obs41528 90.31 %

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