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

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Basic information

Entry
Database: PDB / ID: 9qgc
TitleCrystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant Q204K
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
ACETATE ION / FLAVIN MONONUCLEOTIDE / All1865 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.239 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

Downloads & links

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Assembly

Deposited unit
D: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6139
Polymers40,7251
Non-polymers8888
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint17 kcal/mol
Surface area13230 Å2
Unit cell
Length a, b, c (Å)55.36, 68.56, 90.04
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein All1865 protein


Mass: 40725.387 Da / Num. of mol.: 1 / Mutation: Q204K
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
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.37 %
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: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.239→50 Å / Num. obs: 97454 / % possible obs: 99.5 % / Redundancy: 9.31 % / CC1/2: 0.999 / Net I/σ(I): 15.05
Reflection shellResolution: 1.24→1.31 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 15219 / CC1/2: 0.522 / % possible all: 97

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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: 1.239→47.159 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.868 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.04 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1633 4873 5 %
Rwork0.1289 92581 -
all0.131 --
obs-97454 99.465 %
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: 18.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.894 Å2-0 Å2-0 Å2
2---0.898 Å20 Å2
3---1.792 Å2
Refinement stepCycle: LAST / Resolution: 1.239→47.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 59 467 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123092
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.8144236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.024524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23210472
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.58410146
X-RAY DIFFRACTIONr_chiral_restr0.120.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022463
X-RAY DIFFRACTIONr_nbd_refined0.2110.21590
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2374
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.242
X-RAY DIFFRACTIONr_mcbond_it4.0111.4551541
X-RAY DIFFRACTIONr_mcangle_it5.5722.631960
X-RAY DIFFRACTIONr_scbond_it6.1551.6921551
X-RAY DIFFRACTIONr_scangle_it8.3953.0042276
X-RAY DIFFRACTIONr_lrange_it13.10422.1665138
X-RAY DIFFRACTIONr_rigid_bond_restr4.92733092
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
1.239-1.2710.3133390.29464460.29571760.9080.92194.55130.281
1.271-1.3060.2513450.25365480.25369690.9390.94498.90950.233
1.306-1.3430.2373400.20564650.20768060.9560.96499.98530.182
1.343-1.3850.2443310.19362940.19566290.9560.97199.93970.167
1.385-1.430.1943200.15960700.16163910.9650.9899.98440.133
1.43-1.480.1863090.14458750.14661850.970.98499.98380.116
1.48-1.5360.1793000.12657070.12960100.9770.98899.95010.1
1.536-1.5990.1592870.11654510.11857430.980.9999.91290.09
1.599-1.670.1392780.09352790.09555570.9840.9941000.074
1.67-1.7510.1352640.09550210.09752860.9870.99499.98110.076
1.751-1.8460.1582540.09148170.09450740.9850.99599.94090.075
1.846-1.9570.162390.09645520.09948020.9840.99499.77090.081
1.957-2.0920.1532250.09442660.09745000.9850.99599.80.084
2.092-2.260.1612100.10639960.10942090.9850.99399.92870.097
2.26-2.4750.1421950.10936980.11138950.9870.99299.94870.103
2.475-2.7660.1541770.12333640.12435430.9850.9999.94360.122
2.766-3.1920.1591570.13229820.13431390.9840.9891000.137
3.192-3.9050.1331340.11825440.11926860.990.99299.70220.129
3.905-5.5030.1231060.11420160.11421220.9910.9931000.137
5.503-47.1590.222630.20911890.20912540.9760.97699.84050.249

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