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- PDB-5vwb: Y316F mutant of corn root ferredoxin:NADP+ reductase in alternate... -

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Basic information

Entry
Database: PDB / ID: 5vwb
TitleY316F 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 / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase, chloroplastic / ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)36,8994
Polymers35,3461
Non-polymers1,5533
Water9,188510
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)59.306, 59.306, 186.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1009-

HOH

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 35345.996 Da / Num. of mol.: 1 / Mutation: Y361F
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
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: Nov 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→10.834 Å / Num. obs: 32137 / % possible obs: 88.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1 / Num. unique obs: 1058 / % possible all: 30

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→10.834 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 3168 9.88 %
Rwork0.1539 --
obs0.1597 32072 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→10.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 93 510 3033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012661
X-RAY DIFFRACTIONf_angle_d1.1863642
X-RAY DIFFRACTIONf_dihedral_angle_d14.7461608
X-RAY DIFFRACTIONf_chiral_restr0.062378
X-RAY DIFFRACTIONf_plane_restr0.007466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8004-1.82710.4063350.3632279X-RAY DIFFRACTION21
1.8271-1.85550.3761460.3497499X-RAY DIFFRACTION35
1.8555-1.88580.3697730.3368697X-RAY DIFFRACTION51
1.8858-1.91810.34181040.2971014X-RAY DIFFRACTION71
1.9181-1.95280.29951300.28031144X-RAY DIFFRACTION83
1.9528-1.99020.29861370.25941300X-RAY DIFFRACTION94
1.9902-2.03050.29881410.22991386X-RAY DIFFRACTION99
2.0305-2.07440.2381720.2011361X-RAY DIFFRACTION100
2.0744-2.12230.24671390.18181429X-RAY DIFFRACTION99
2.1223-2.17490.23891740.17051352X-RAY DIFFRACTION100
2.1749-2.23320.24741550.16961391X-RAY DIFFRACTION100
2.2332-2.29840.19441700.15491378X-RAY DIFFRACTION99
2.2984-2.37180.23151290.15971427X-RAY DIFFRACTION99
2.3718-2.45560.21351520.15781381X-RAY DIFFRACTION99
2.4556-2.55270.21291380.15121403X-RAY DIFFRACTION99
2.5527-2.66720.20791510.15491412X-RAY DIFFRACTION99
2.6672-2.80550.18911480.14911404X-RAY DIFFRACTION99
2.8055-2.97790.1991620.15621409X-RAY DIFFRACTION99
2.9779-3.20230.21711650.14321398X-RAY DIFFRACTION99
3.2023-3.51450.20731690.13341418X-RAY DIFFRACTION99
3.5145-4.00050.1821550.11751431X-RAY DIFFRACTION99
4.0005-4.95850.14971400.09961484X-RAY DIFFRACTION99
4.9585-10.83430.19621830.13941507X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.6866 Å / Origin y: -24.5376 Å / Origin z: 14.4353 Å
111213212223313233
T0.1646 Å20.0188 Å2-0.0006 Å2-0.1094 Å2-0.008 Å2--0.1335 Å2
L1.1105 °20.0203 °20.5629 °2-0.8761 °2-0.0097 °2--1.4653 °2
S-0.0459 Å °0.044 Å °-0.0384 Å °-0.0167 Å °0.055 Å °-0.0048 Å °0.0733 Å °0.0015 Å °0.004 Å °
Refinement TLS groupSelection details: all

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