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

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Basic information

Entry
Database: PDB / ID: 9qgb
TitleCrystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 (engineered Loop Swap from Achromobacter sp. JA81)
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: 1.27 Å
AuthorsBischoff, D. / Walla, B. / Janowski, R. / Maslakova, A. / Maehler, C. / 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
A: All1865 protein
B: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,65526
Polymers81,4492
Non-polymers2,20624
Water20,7351151
1
A: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,73611
Polymers40,7241
Non-polymers1,01210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: All1865 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,91915
Polymers40,7241
Non-polymers1,19514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.22, 67.78, 91.52
Angle α, β, γ (deg.)90, 93.52, 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: 40724.336 Da / Num. of mol.: 2
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, 1175 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1151 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
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, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.27→48.53 Å / Num. obs: 178747 / % possible obs: 97.52 % / Redundancy: 6.75 % / CC1/2: 0.999 / Net I/σ(I): 15.95
Reflection shellResolution: 1.27→1.34 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 26180 / CC1/2: 0.649 / % possible all: 90.9

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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: 1.27→48.528 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.385 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.044 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1614 8663 5 %
Rwork0.1302 164582 -
all0.132 --
obs-173245 97.739 %
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: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.513 Å20 Å2-0.444 Å2
2--0.349 Å20 Å2
3---0.217 Å2
Refinement stepCycle: LAST / Resolution: 1.27→48.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 144 1151 6785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126042
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.8158249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.943543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02210897
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.07610289
X-RAY DIFFRACTIONr_chiral_restr0.120.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024786
X-RAY DIFFRACTIONr_nbd_refined0.2110.23102
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2827
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2580.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.272
X-RAY DIFFRACTIONr_mcbond_it3.8961.2133000
X-RAY DIFFRACTIONr_mcangle_it5.332.1963793
X-RAY DIFFRACTIONr_scbond_it5.8071.4243042
X-RAY DIFFRACTIONr_scangle_it7.7342.5214456
X-RAY DIFFRACTIONr_lrange_it13.29520.14710136
X-RAY DIFFRACTIONr_rigid_bond_restr4.99836042
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
1.27-1.3030.3375600.319106300.32130720.9510.9685.60280.308
1.303-1.3390.3066180.281117450.282126880.9580.97297.43850.266
1.339-1.3770.2536160.226117110.228124240.9750.98299.21930.208
1.377-1.420.2085950.177113010.179120270.9820.98898.91080.158
1.42-1.4660.1865720.136108600.138116030.9820.99198.52620.115
1.466-1.5180.1465560.105105610.107113030.9870.99498.35440.086
1.518-1.5750.1385350.09101800.093109060.9880.99598.24870.075
1.575-1.6390.1335130.08597430.087104320.9890.99698.31290.072
1.639-1.7120.1275010.08595140.087100770.9910.99699.38470.074
1.712-1.7950.1274780.08890810.0996230.9910.99699.33490.08
1.795-1.8920.1444530.10386190.10591570.990.99699.07170.096
1.892-2.0070.1494270.11981010.1286550.990.99698.53260.113
2.007-2.1450.1494010.12276130.12381620.990.99598.18670.118
2.145-2.3170.1423720.11570750.11675880.990.99498.14180.112
2.317-2.5370.1453510.1166620.11270180.9880.99399.92880.11
2.537-2.8360.1553140.1259840.12263040.9850.99199.90480.123
2.836-3.2730.1482810.12153230.12256260.9870.99299.6090.128
3.273-4.0040.1322310.10943970.1147640.9910.99397.14530.123
4.004-5.6430.1721830.14934790.1537120.9890.99398.6530.173
5.643-48.5280.2741060.2720030.2721090.9850.9821000.304

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