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- PDB-4k1x: Ferredoxin-NADP(H) Reductase mutant with Ala 266 replaced by Tyr ... -

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Basic information

Entry
Database: PDB / ID: 4k1x
TitleFerredoxin-NADP(H) Reductase mutant with Ala 266 replaced by Tyr (A266Y) and residues 267-272 deleted.
ComponentsNADPH:ferredoxin reductase
KeywordsOXIDOREDUCTASE / Reductase / NADP+ binding
Function / homology
Function and homology information


flavodoxin-NADP+ reductase / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding / cytoplasm
Similarity search - Function
Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding 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, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding 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 / Flavodoxin/ferredoxin--NADP reductase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBortolotti, A. / Sanchez-Azqueta, A. / Maya, C.M. / Velazquez-Campoy, A. / Hermoso, J.A. / Cortez, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: The C-terminal extension of bacterial flavodoxin-reductases: Involvement in the hydride transfer mechanism from the coenzyme.
Authors: Bortolotti, A. / Sanchez-Azqueta, A. / Maya, C.M. / Velazquez-Campoy, A. / Hermoso, J.A. / Medina, M. / Cortez, N.
History
DepositionApr 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: NADPH:ferredoxin reductase
B: NADPH:ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4445
Polymers56,7772
Non-polymers1,6673
Water4,053225
1
A: NADPH:ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2703
Polymers28,3891
Non-polymers8822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH:ferredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1742
Polymers28,3891
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.970, 74.970, 188.610
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 NADPH:ferredoxin reductase


Mass: 28388.531 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 16-272 / Mutation: A266Y, 267-272 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: fpr / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L6V3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 225 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 267-272 WERE DELETED

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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: 2.69 Å3/Da / Density % sol: 54.36 % / Mosaicity: 0.21 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% (wt/vol) PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.7→38.152 Å / Num. all: 68570 / Num. obs: 68570 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rsym value: 0.108 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.7910.90.5930.5651.310713298370.1790.5930.5654.7100
1.79-1.910.90.4030.3841.910220193770.1210.4030.3846.9100
1.9-2.0310.90.2560.2443.19605288290.0770.2560.24410.3100
2.03-2.1910.90.1720.1644.58916382030.0520.1720.16414.1100
2.19-2.410.80.1280.12268222476060.0390.1280.12217.6100
2.4-2.6910.70.1020.0977.57380168700.0310.1020.09719.7100
2.69-3.110.60.090.0867.76510061210.0270.090.08624.8100
3.1-3.810.20.070.0679.25343052270.0220.070.06731.9100
3.8-5.3810.10.0460.04413.14152041120.0140.0460.04436.199.9
5.38-38.15210.20.0470.04412.42432023880.0140.0470.04433.399.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.152 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9155 / SU ML: 0.44 / σ(F): 1.33 / Phase error: 14.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 2009 2.93 %random
Rwork0.1769 ---
all0.2051 68556 --
obs0.1771 68499 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.572 Å2 / ksol: 0.441 e/Å3
Displacement parametersBiso max: 97.26 Å2 / Biso mean: 18.5294 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.0885 Å20 Å2-0 Å2
2---0.0885 Å20 Å2
3----2.177 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 111 225 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124202
X-RAY DIFFRACTIONf_angle_d1.6585716
X-RAY DIFFRACTIONf_chiral_restr0.387630
X-RAY DIFFRACTIONf_plane_restr0.008722
X-RAY DIFFRACTIONf_dihedral_angle_d12.7751548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.74250.19051380.201346914829
1.7425-1.78960.1691430.190146814824
1.7896-1.84230.16211410.17346504791
1.8423-1.90170.17461410.167346784819
1.9017-1.96970.16461420.160747554897
1.9697-2.04860.17431430.162346694812
2.0486-2.14180.16821410.165147384879
2.1418-2.25470.17031410.157646984839
2.2547-2.39590.15441420.164147114853
2.3959-2.58090.20371460.185547844930
2.5809-2.84060.21321430.208147364879
2.8406-3.25140.21491410.211248264967
3.2514-4.09570.17471480.16448124960
4.0957-38.1620.17961590.16950615220

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