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

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Basic information

Entry
Database: PDB / ID: 9qgd
TitleCrystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant Q350K
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)41,5258
Polymers40,7251
Non-polymers7997
Water9,278515
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint2 kcal/mol
Surface area13120 Å2
Unit cell
Length a, b, c (Å)55.32, 68.38, 89.87
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules D

#1: Protein All1865 protein


Mass: 40725.387 Da / Num. of mol.: 1 / Mutation: T350K
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, 522 molecules

#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.: 4 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
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: 95888 / % possible obs: 98.5 % / Redundancy: 12.57 % / CC1/2: 1 / Net I/σ(I): 21.81
Reflection shellResolution: 1.239→1.31 Å / Redundancy: 9.88 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 14216 / CC1/2: 0.734 / % possible all: 91.3

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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: 1.239→47.11 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.487 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.037 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.149 4795 5.001 %
Rwork0.1189 91093 -
all0.12 --
obs-95888 98.485 %
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: 20.034 Å2
Baniso -1Baniso -2Baniso -3
1--1.173 Å2-0 Å2-0 Å2
2---0.993 Å2-0 Å2
3---2.165 Å2
Refinement stepCycle: LAST / Resolution: 1.239→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 52 515 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123131
X-RAY DIFFRACTIONr_angle_refined_deg2.0531.8114303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.389524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35710477
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7410150
X-RAY DIFFRACTIONr_chiral_restr0.1220.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022519
X-RAY DIFFRACTIONr_nbd_refined0.2260.21700
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2423
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.250
X-RAY DIFFRACTIONr_mcbond_it4.5391.5471566
X-RAY DIFFRACTIONr_mcangle_it6.1022.7952000
X-RAY DIFFRACTIONr_scbond_it71.7951565
X-RAY DIFFRACTIONr_scangle_it9.3033.1852303
X-RAY DIFFRACTIONr_lrange_it16.43325.3465345
X-RAY DIFFRACTIONr_rigid_bond_restr5.70433131
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
1.239-1.2710.2853040.25357820.25571090.9480.95285.60980.23
1.271-1.3060.2033290.21262450.21169140.9650.97295.08240.184
1.306-1.3440.1933390.17764450.17767850.9760.98199.98530.15
1.344-1.3850.1883280.15462250.15665540.970.98699.98470.127
1.385-1.430.1673190.13460550.13663750.9830.9999.98430.107
1.43-1.4810.1443060.11358280.11561340.9870.9921000.089
1.481-1.5360.1452970.10756380.10959590.9850.99499.59720.084
1.536-1.5990.1352850.09154180.09357550.9880.99699.09640.072
1.599-1.670.1232750.07552240.07755010.990.99799.96360.061
1.67-1.7520.1372640.08150010.08352650.9890.9971000.068
1.752-1.8460.1162510.0847810.08250330.9920.99699.98010.069
1.846-1.9580.1332390.09245320.09447710.9880.9951000.083
1.958-2.0930.1242240.09942570.10144860.9910.99599.88850.094
2.093-2.260.1442080.10239620.10441850.9880.99599.64160.1
2.26-2.4750.1451930.10836680.1138610.9880.9931000.11
2.475-2.7670.1551760.11833450.1235230.9840.99199.94320.126
2.767-3.1930.1731560.12429620.12731200.9820.99199.93590.138
3.193-3.9060.1131340.10525380.10626760.9920.99399.85050.125
3.906-5.5050.1381050.11920030.1221080.9910.9931000.149
5.505-47.110.231630.24611840.24512480.9520.97799.91990.291

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