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- PDB-5vw7: NADPH soak of Y316A mutant of corn root ferredoxin:NADP+ reductase -

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Basic information

Entry
Database: PDB / ID: 5vw7
TitleNADPH soak of Y316A 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 / 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
ACETATE ION / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.608 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8845
Polymers35,2701
Non-polymers1,6144
Water9,548530
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)59.188, 59.188, 188.032
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-894-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferredoxin--NADP reductase


Mass: 35269.902 Da / Num. of mol.: 1 / Mutation: Y327A
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

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Non-polymers , 5 types, 534 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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
#5: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.37 %
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 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→49.45 Å / Num. obs: 50821 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 24.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 6 / Num. unique obs: 4336 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LO8

3lo8


Resolution: 1.608→49.454 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1556 5122 10.09 %
Rwork0.1306 --
obs0.1332 50752 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.608→49.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 106 530 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092718
X-RAY DIFFRACTIONf_angle_d1.173732
X-RAY DIFFRACTIONf_dihedral_angle_d15.5591667
X-RAY DIFFRACTIONf_chiral_restr0.064387
X-RAY DIFFRACTIONf_plane_restr0.007480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.608-1.62630.19731670.16191480X-RAY DIFFRACTION99
1.6263-1.64540.17741600.15291522X-RAY DIFFRACTION100
1.6454-1.66550.17231650.14761485X-RAY DIFFRACTION100
1.6655-1.68660.18561700.14571508X-RAY DIFFRACTION100
1.6866-1.70880.16781700.13551481X-RAY DIFFRACTION100
1.7088-1.73220.15811750.14011483X-RAY DIFFRACTION100
1.7322-1.75690.17991700.14051489X-RAY DIFFRACTION100
1.7569-1.78310.17821880.13961478X-RAY DIFFRACTION100
1.7831-1.8110.15531850.14251477X-RAY DIFFRACTION100
1.811-1.84070.17391900.13461508X-RAY DIFFRACTION100
1.8407-1.87240.17611740.13271469X-RAY DIFFRACTION100
1.8724-1.90650.17511560.12861550X-RAY DIFFRACTION100
1.9065-1.94320.1621690.12641462X-RAY DIFFRACTION100
1.9432-1.98280.12461670.12581543X-RAY DIFFRACTION100
1.9828-2.02590.14821480.1251502X-RAY DIFFRACTION100
2.0259-2.07310.14771870.12661513X-RAY DIFFRACTION100
2.0731-2.12490.13291510.13181529X-RAY DIFFRACTION100
2.1249-2.18240.15361950.12341494X-RAY DIFFRACTION100
2.1824-2.24660.15051670.12281496X-RAY DIFFRACTION100
2.2466-2.31910.15971660.12581516X-RAY DIFFRACTION100
2.3191-2.4020.15161690.12981533X-RAY DIFFRACTION100
2.402-2.49820.15921610.12471543X-RAY DIFFRACTION100
2.4982-2.61180.14731480.1221549X-RAY DIFFRACTION100
2.6118-2.74950.13271680.11871535X-RAY DIFFRACTION100
2.7495-2.92180.15221770.12631528X-RAY DIFFRACTION100
2.9218-3.14730.14341690.12521548X-RAY DIFFRACTION100
3.1473-3.4640.15281750.12121560X-RAY DIFFRACTION100
3.464-3.96510.14911790.1131569X-RAY DIFFRACTION100
3.9651-4.99480.11981520.1151619X-RAY DIFFRACTION100
4.9948-49.47710.20822040.19231661X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.7873 Å / Origin y: 17.6322 Å / Origin z: 13.4753 Å
111213212223313233
T0.0885 Å2-0.0192 Å20.0361 Å2-0.1605 Å2-0.0302 Å2--0.1376 Å2
L0.3091 °20.1389 °20.0268 °2-0.5663 °20.0652 °2--1.4563 °2
S-0.0839 Å °0.0732 Å °-0.0527 Å °-0.0925 Å °0.0749 Å °-0.0867 Å °0.1155 Å °0.1798 Å °0.0186 Å °
Refinement TLS groupSelection details: all

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