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- PDB-5vw4: Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ r... -

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Basic information

Entry
Database: PDB / ID: 5vw4
TitleNicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ reductase
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / flavoenzyme / hydride transfer / photosynthesis / active site compression
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / NADPH binding / photosynthesis / chloroplast / electron transport chain / electron transfer activity / nucleotide binding
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 / NICOTINAMIDE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.351 Å
AuthorsKean, K.M. / Carpenter, R.A. / Hall, A.R. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM119227 United States
National Science Foundation (NSF, United States)MCB-9982727 United States
CitationJournal: FEBS J. / Year: 2017
Title: High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily.
Authors: Kean, K.M. / Carpenter, R.A. / Pandini, V. / Zanetti, G. / Hall, A.R. / Faber, R. / Aliverti, A. / Karplus, P.A.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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.ptnr2_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,2184
Polymers35,2861
Non-polymers9323
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.894, 58.894, 184.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-245-

GLY

21A-899-

HOH

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 35285.902 Da / Num. of mol.: 1 / Mutation: Y327S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli)
References: UniProt: Q41736, UniProt: B4G043*PLUS, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22-24% PEG 8000, 0.1 M sodium cacodylate (pH 6-7), 0.18-0.22 M magnesium acetate, 100 mM nicotinamide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→51 Å / Num. obs: 75008 / % possible obs: 91 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.2
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9295 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LO8

3lo8


Resolution: 1.351→51.004 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 7589 10.13 %
Rwork0.1346 --
obs0.1385 74924 90.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.351→51.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 63 484 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092724
X-RAY DIFFRACTIONf_angle_d1.0133729
X-RAY DIFFRACTIONf_dihedral_angle_d18.7331062
X-RAY DIFFRACTIONf_chiral_restr0.08386
X-RAY DIFFRACTIONf_plane_restr0.007488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3511-1.36640.25732030.20021743X-RAY DIFFRACTION71
1.3664-1.38250.23552090.19061878X-RAY DIFFRACTION78
1.3825-1.39940.23562200.18641936X-RAY DIFFRACTION78
1.3994-1.41710.21192180.17531891X-RAY DIFFRACTION79
1.4171-1.43570.23921960.17261993X-RAY DIFFRACTION80
1.4357-1.45540.22962630.16431940X-RAY DIFFRACTION83
1.4554-1.47620.19752610.15561995X-RAY DIFFRACTION82
1.4762-1.49820.19682320.15261995X-RAY DIFFRACTION82
1.4982-1.52170.19142280.14472081X-RAY DIFFRACTION85
1.5217-1.54660.19352190.13482125X-RAY DIFFRACTION86
1.5466-1.57330.17452360.12672119X-RAY DIFFRACTION87
1.5733-1.60190.17322400.12532170X-RAY DIFFRACTION88
1.6019-1.63270.17342320.12122218X-RAY DIFFRACTION90
1.6327-1.6660.17212510.11642198X-RAY DIFFRACTION91
1.666-1.70230.15242570.11542269X-RAY DIFFRACTION92
1.7023-1.74190.15452610.12072242X-RAY DIFFRACTION93
1.7419-1.78540.16742810.11342283X-RAY DIFFRACTION93
1.7854-1.83370.17692860.10962276X-RAY DIFFRACTION94
1.8337-1.88770.16582550.11382356X-RAY DIFFRACTION95
1.8877-1.94860.14362510.11372317X-RAY DIFFRACTION94
1.9486-2.01820.15582630.11162489X-RAY DIFFRACTION100
2.0182-2.0990.14822830.10422481X-RAY DIFFRACTION100
2.099-2.19460.14152900.10332455X-RAY DIFFRACTION100
2.1946-2.31030.15712750.10952494X-RAY DIFFRACTION100
2.3103-2.4550.14922630.11542529X-RAY DIFFRACTION100
2.455-2.64460.16932620.12662505X-RAY DIFFRACTION100
2.6446-2.91070.17312880.13082517X-RAY DIFFRACTION100
2.9107-3.33180.16992860.13922530X-RAY DIFFRACTION100
3.3318-4.19740.15692820.13772600X-RAY DIFFRACTION100
4.1974-51.040.20412980.18832710X-RAY DIFFRACTION100

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