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- PDB-9qgf: Crystal structure of an NADH-accepting ene reductase variant Nost... -

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Basic information

Entry
Database: PDB / ID: 9qgf
TitleCrystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant T354K
ComponentsAll1865 protein
KeywordsOXIDOREDUCTASE / Ene reductase / Cyanobacteria / Achromobacter sp. JA81 Loop / Alkene reductase / Formate Dehydrogenase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / metal ion binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / All1865 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.444 Å
AuthorsBischoff, D. / Walla, B. / Janowski, R. / Maslakova, A. / Niessing, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE2715/14-2 Germany
CitationJournal: Biomolecules / Year: 2025
Title: Rational Introduction of Electrostatic Interactions at Crystal Contacts to Enhance Protein Crystallization of an Ene Reductase.
Authors: Walla, B. / Maslakova, A. / Bischoff, D. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
History
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: All1865 protein
B: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,28515
Polymers81,5052
Non-polymers1,78013
Water16,214900
1
A: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6748
Polymers40,7521
Non-polymers9217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6127
Polymers40,7521
Non-polymers8596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.5, 68.08, 91.71
Angle α, β, γ (deg.)90, 93.7, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein All1865 protein


Mass: 40752.414 Da / Num. of mol.: 2 / Mutation: D354K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Gene: all1865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YVV8

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Non-polymers , 6 types, 913 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1I6V / 1-[(6~{R})-3,3-diethanoyl-6-methyl-cyclohexa-1,4-dien-1-yl]ethanone


Mass: 220.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 25 mM sodium phosphate pH 7.2, 75 mM NaCl, 25 mM Tris-HCl pH 8.5, 0.1 M NH4Cl, 5 mM CaCl2, 15% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.44→48.8 Å / Num. obs: 120777 / % possible obs: 98.8 % / Redundancy: 6.84 % / CC1/2: 0.998 / Net I/σ(I): 9.63
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 6.54 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 19339 / CC1/2: 0.526 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSJun 30, 2024data reduction
XDSJun 30, 2024data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.444→48.799 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.191 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.067 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1868 6039 5 %
Rwork0.1418 114736 -
all0.144 --
obs-120775 98.764 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.436 Å2
Baniso -1Baniso -2Baniso -3
1--0.397 Å20 Å20.427 Å2
2---0.74 Å20 Å2
3---1.073 Å2
Refinement stepCycle: LAST / Resolution: 1.444→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 118 900 6496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126032
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.8218268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.983550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44810912
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.410286
X-RAY DIFFRACTIONr_chiral_restr0.1290.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024806
X-RAY DIFFRACTIONr_nbd_refined0.2120.23130
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2679
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.259
X-RAY DIFFRACTIONr_mcbond_it3.7921.4112996
X-RAY DIFFRACTIONr_mcangle_it5.4132.5463794
X-RAY DIFFRACTIONr_scbond_it5.3441.5853036
X-RAY DIFFRACTIONr_scangle_it7.5022.8364474
X-RAY DIFFRACTIONr_lrange_it13.4120.17310034
X-RAY DIFFRACTIONr_rigid_bond_restr4.54636032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.444-1.4810.3314440.30484350.30590190.9190.93798.44770.298
1.481-1.5220.2654290.24481470.24587170.950.96298.38250.231
1.522-1.5660.294070.22777460.2385730.9450.96695.10090.209
1.566-1.6140.2354120.19278260.19482790.9610.97699.50480.169
1.614-1.6670.2014010.15776170.15980270.9760.98599.88790.135
1.667-1.7250.2173900.14174030.14578120.9670.98899.75680.119
1.725-1.790.1963740.12871140.13175130.9760.9999.66720.104
1.79-1.8630.1933600.12168330.12472130.9750.99199.72270.1
1.863-1.9460.1613450.1165590.11269360.9840.99399.53860.093
1.946-2.0410.1673280.11962380.12166650.9840.99398.51460.104
2.041-2.1510.1672980.11756600.11962790.9850.99394.88770.104
2.151-2.2810.172980.11556620.11859790.9820.99399.68220.104
2.281-2.4380.1782820.11753470.1256320.9820.99299.94670.108
2.438-2.6330.1792610.12649720.12952390.980.9999.88550.121
2.633-2.8830.1812400.12845560.1348040.980.9999.83350.126
2.883-3.2220.1542180.13541340.13643860.9870.98999.22480.135
3.222-3.7180.1631910.1336430.13238900.9830.9998.56040.136
3.718-4.5470.1731590.12430090.12732780.9850.99196.64430.14
4.547-6.4030.1551280.15424310.15425600.9870.98999.96090.177
6.403-48.7990.221740.19114050.19314840.980.98299.66310.217

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