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- PDB-2bmw: Ferredoxin: NADP+ Reductase Mutant With Thr 155 Replaced By Gly, ... -

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Basic information

Entry
Database: PDB / ID: 2bmw
TitleFerredoxin: NADP+ Reductase Mutant With Thr 155 Replaced By Gly, Ala 160 Replaced By Thr, Leu 263 Replaced By Pro, Arg 264 Replaced By Pro and Gly 265 Replaced by Pro (T155G-A160T-L263P-R264P-G265P)
ComponentsFERREDOXIN--NADP REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / REDUCTASE REDUCTASE / PHYCOBILISOME / THYLAKOID
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / 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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMartinez-Julvez, M. / Hermoso, J.A. / Perez-Dorado, I. / Medina, M. / Tejero, J. / Gomez-Moreno, C.
Citation
Journal: Biochemistry / Year: 2009
Title: Protein Motifs Involved in Coenzyme Interaction and Enzymatic Efficiency in Anabaena Ferredoxin-Nadp+ Reductase.
Authors: Peregrina, J.R. / Herguedas, B. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M.
#1: Journal: Biophys.Chem. / Year: 2005
Title: Towards a New Therapeutic Target: Helicobacter Pylori Flavodoxin
Authors: Cremades, N. / Bueno, M. / Toja, M. / Sancho, J.
History
DepositionMar 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)35,0043
Polymers34,1231
Non-polymers8822
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.970, 85.970, 96.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FERREDOXIN--NADP REDUCTASE / FERREDOXIN-NADP+ REDUCTASE / FNR


Mass: 34122.781 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-440 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTATIONS T155G, A160T, L263P, R264P AND G265P / Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.46 Å3/Da / Density % sol: 49.66 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97954
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.5→29.5 Å / Num. obs: 64511 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 8.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.32 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUE

1que


Resolution: 1.5→28.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1616756 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FIRST 8 RESIDUES WERE NOT FOUND IN THE ELECTRONIC DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4558 7.1 %RANDOM
Rwork0.185 ---
obs0.185 64244 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4346 Å2 / ksol: 0.337619 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0.36 Å20 Å2
2--1.83 Å20 Å2
3----3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 58 586 2978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 744 7 %
Rwork0.206 9939 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD_XPLOR_PAR.TXTFAD_XPLOR_TOP.TXT
X-RAY DIFFRACTION3SO4_XPLOR_PAR.TXTSO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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