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- PDB-5vw8: NADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductas... -

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Basic information

Entry
Database: PDB / ID: 5vw8
TitleNADP+ soak of Y316S mutant of corn root ferredoxin:NADP+ reductase in alternate space group
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 / chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / NADPH dehydrogenase activity / ferredoxin-NADP+ reductase activity / NADPH binding / photosynthesis / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.808 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 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 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 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Oct 23, 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)36,8394
Polymers35,2861
Non-polymers1,5533
Water5,350297
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)58.867, 58.867, 185.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 53.1 %
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: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→39.3 Å / Num. obs: 35032 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5039 / % possible all: 99.9

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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: 1.808→39.295 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 3484 9.97 %
Rwork0.1719 --
obs0.1757 34947 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.808→39.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 102 297 2811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092714
X-RAY DIFFRACTIONf_angle_d1.2723723
X-RAY DIFFRACTIONf_dihedral_angle_d18.2581629
X-RAY DIFFRACTIONf_chiral_restr0.062384
X-RAY DIFFRACTIONf_plane_restr0.007472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8081-1.83290.30971570.28531242X-RAY DIFFRACTION99
1.8329-1.85910.31861410.25141204X-RAY DIFFRACTION100
1.8591-1.88690.2781330.23711261X-RAY DIFFRACTION100
1.8869-1.91630.21331340.21251216X-RAY DIFFRACTION100
1.9163-1.94780.27721360.1771250X-RAY DIFFRACTION100
1.9478-1.98130.21061320.18551233X-RAY DIFFRACTION100
1.9813-2.01740.20781250.17371249X-RAY DIFFRACTION100
2.0174-2.05620.2291600.17141213X-RAY DIFFRACTION100
2.0562-2.09810.20591240.15731269X-RAY DIFFRACTION100
2.0981-2.14380.18481450.15311206X-RAY DIFFRACTION100
2.1438-2.19360.19431430.15661255X-RAY DIFFRACTION100
2.1936-2.24850.19111400.16051237X-RAY DIFFRACTION100
2.2485-2.30930.18461380.15041245X-RAY DIFFRACTION99
2.3093-2.37720.1921350.14991250X-RAY DIFFRACTION100
2.3772-2.45390.21631270.15211277X-RAY DIFFRACTION100
2.4539-2.54160.22041280.16161261X-RAY DIFFRACTION100
2.5416-2.64330.22251330.16251250X-RAY DIFFRACTION100
2.6433-2.76360.21281350.16421261X-RAY DIFFRACTION100
2.7636-2.90930.19091540.16551264X-RAY DIFFRACTION100
2.9093-3.09150.20051350.18271282X-RAY DIFFRACTION100
3.0915-3.33010.20761510.18621242X-RAY DIFFRACTION100
3.3301-3.6650.24461410.18221318X-RAY DIFFRACTION100
3.665-4.19480.21611390.16781292X-RAY DIFFRACTION100
4.1948-5.28290.18171340.14571318X-RAY DIFFRACTION100
5.2829-39.3040.1851640.18581368X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.4028 Å / Origin y: -25.403 Å / Origin z: 16.3179 Å
111213212223313233
T0.2104 Å2-0.0767 Å20.0492 Å2-0.1737 Å20.0121 Å2--0.1583 Å2
L1.0472 °20.1062 °20.3069 °2-0.9732 °2-0.2299 °2--1.4343 °2
S-0.0919 Å °-0.0644 Å °-0.1157 Å °-0.1263 Å °0.0127 Å °-0.106 Å °0.0438 Å °0.1038 Å °0.0824 Å °
Refinement TLS groupSelection details: all

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