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- PDB-5vw6: NADP+ soak of Y316A mutant of corn root ferredoxin:NADP+ reductase -

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Basic information

Entry
Database: PDB / ID: 5vw6
TitleNADP+ 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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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)36,8234
Polymers35,2701
Non-polymers1,5533
Water8,125451
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)58.669, 58.669, 186.734
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-858-

HOH

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 35269.902 Da / Num. of mol.: 1 / Mutation: Y316A
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 / 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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
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: 1.5→49.02 Å / Num. obs: 44421 / % possible obs: 72.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 1371 / % possible all: 23

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Processing

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

3lo8


Resolution: 1.5→49.02 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1853 4249 9.57 %
Rwork0.1486 --
obs0.1521 44412 73.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 102 451 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092629
X-RAY DIFFRACTIONf_angle_d1.1833600
X-RAY DIFFRACTIONf_dihedral_angle_d15.471579
X-RAY DIFFRACTIONf_chiral_restr0.061373
X-RAY DIFFRACTIONf_plane_restr0.007463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.4382360.3862307X-RAY DIFFRACTION17
1.5171-1.53490.3394490.4074401X-RAY DIFFRACTION23
1.5349-1.55370.4276630.3677513X-RAY DIFFRACTION29
1.5537-1.57330.332680.3007622X-RAY DIFFRACTION35
1.5733-1.5940.2837750.2841736X-RAY DIFFRACTION40
1.594-1.61590.259140.2756986X-RAY DIFFRACTION50
1.6159-1.63890.2209680.26441177X-RAY DIFFRACTION62
1.6389-1.66340.29671410.25261298X-RAY DIFFRACTION72
1.6634-1.68940.25611650.24141381X-RAY DIFFRACTION77
1.6894-1.71710.25621460.21831498X-RAY DIFFRACTION82
1.7171-1.74670.24461710.21111514X-RAY DIFFRACTION84
1.7467-1.77850.27071800.20221535X-RAY DIFFRACTION85
1.7785-1.81270.23081250.19621537X-RAY DIFFRACTION84
1.8127-1.84970.23481670.18381535X-RAY DIFFRACTION85
1.8497-1.88990.19441700.16861540X-RAY DIFFRACTION84
1.8899-1.93390.19621600.15321504X-RAY DIFFRACTION84
1.9339-1.98220.17751900.13571526X-RAY DIFFRACTION86
1.9822-2.03580.17552440.13581511X-RAY DIFFRACTION86
2.0358-2.09570.15562180.13831521X-RAY DIFFRACTION86
2.0957-2.16340.15351380.13681600X-RAY DIFFRACTION87
2.1634-2.24070.17761490.13451568X-RAY DIFFRACTION86
2.2407-2.33040.17391850.13461575X-RAY DIFFRACTION86
2.3304-2.43650.16991940.13231585X-RAY DIFFRACTION87
2.4365-2.56490.1581510.13391603X-RAY DIFFRACTION86
2.5649-2.72560.16451780.12731577X-RAY DIFFRACTION86
2.7256-2.9360.17391880.12791576X-RAY DIFFRACTION86
2.936-3.23140.17531670.12311583X-RAY DIFFRACTION85
3.2314-3.69890.14021630.10881635X-RAY DIFFRACTION86
3.6989-4.65970.15351640.11011612X-RAY DIFFRACTION84
4.6597-49.05260.24571320.18511607X-RAY DIFFRACTION77
Refinement TLS params.Method: refined / Origin x: -15.6202 Å / Origin y: 17.6507 Å / Origin z: 13.3984 Å
111213212223313233
T0.0953 Å2-0.0207 Å20.0317 Å2-0.1655 Å2-0.0252 Å2--0.1395 Å2
L0.3356 °20.1442 °20.0047 °2-0.6551 °20.1432 °2--1.7066 °2
S-0.0736 Å °0.0922 Å °-0.05 Å °-0.0949 Å °0.0772 Å °-0.0833 Å °0.1258 Å °0.1701 Å °0.0106 Å °
Refinement TLS groupSelection details: all

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