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

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Basic information

Entry
Database: PDB / ID: 9qge
TitleCrystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant D352K
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: 1.433 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)82,6089
Polymers81,4772
Non-polymers1,1317
Water15,889882
1
A: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2924
Polymers40,7381
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3155
Polymers40,7381
Non-polymers5774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.4, 68.16, 91.63
Angle α, β, γ (deg.)90, 94.07, 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: 40738.430 Da / Num. of mol.: 2 / Mutation: D352K
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 , 5 types, 889 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 41.93 %
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: 1.43→50 Å / Num. obs: 122540 / % possible obs: 98.3 % / Redundancy: 5.12 % / CC1/2: 0.997 / Net I/σ(I): 10.36
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 4.98 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 19435 / CC1/2: 0.565 / % possible all: 96.8

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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: 1.433→48.849 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.836 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.068 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1949 6127 5 %
Rwork0.1508 116413 -
all0.153 --
obs-122540 98.263 %
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: 17.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.505 Å2
2---1.042 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.433→48.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 73 882 6447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125937
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.818142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.785542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42910900
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.58310278
X-RAY DIFFRACTIONr_chiral_restr0.1130.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024710
X-RAY DIFFRACTIONr_nbd_refined0.2090.22962
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2621
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.252
X-RAY DIFFRACTIONr_mcbond_it3.8131.4252979
X-RAY DIFFRACTIONr_mcangle_it5.4892.5693764
X-RAY DIFFRACTIONr_scbond_it5.3331.5972958
X-RAY DIFFRACTIONr_scangle_it7.4682.8554378
X-RAY DIFFRACTIONr_lrange_it12.18619.629689
X-RAY DIFFRACTIONr_rigid_bond_restr4.33335937
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
1.433-1.4710.3354340.29982630.30191750.930.94994.79020.288
1.471-1.5110.3024420.24883940.25189880.9580.96998.30890.234
1.511-1.5550.2254170.2179280.2186640.9710.97796.31810.192
1.555-1.6020.2274160.18478930.18784700.9720.98498.09920.163
1.602-1.6550.24110.15578020.15782210.9740.98899.90270.133
1.655-1.7130.1963940.12974880.13278950.980.99199.83530.108
1.713-1.7770.1953820.11772640.12176740.9760.99299.63510.097
1.777-1.850.1773670.10869830.11173750.9780.99399.6610.092
1.85-1.9320.1733500.1266400.12370650.9820.99398.93840.108
1.932-2.0260.1923310.13962800.14267370.980.99398.12970.131
2.026-2.1360.1923070.14858420.15164820.9820.99294.86270.143
2.136-2.2650.1763000.13756960.13960720.9810.99198.74840.133
2.265-2.4210.1782850.12454250.12757260.9810.99199.72060.122
2.421-2.6140.1782670.1350580.13253560.980.9999.42120.129
2.614-2.8630.1872440.13646470.13849170.980.98899.47120.139
2.863-3.1990.22210.15142030.15444550.9750.98599.30420.16
3.199-3.6920.1681950.14136950.14239700.9830.98797.98490.156
3.692-4.5150.1611600.14130480.14233320.9870.98996.27850.163
4.515-6.3580.2171290.17924570.18126210.9830.98698.66460.205
6.358-48.8490.268750.23914070.24115080.9740.98198.27590.28

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