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- PDB-5nux: Thermus scotoductus SA-01 Ene-reductase double mutant TsER_C25D_I67T -

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Basic information

Entry
Database: PDB / ID: 5nux
TitleThermus scotoductus SA-01 Ene-reductase double mutant TsER_C25D_I67T
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / Ene-reductase Old yellow enzyme C25D_I67T
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chromate reductase
Similarity search - Component
Biological speciesThermus scotoductus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOpperman, D.J. / Hoebenreich, S. / Nett, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
State of HesseLOEWE research cluster SynChemBio Germany
CitationJournal: Mol Catal / Year: 2021
Title: A robust and stereocomplementary panel of ene-reductase variants for gram-scale asymmetric hydrogenation
Authors: Nett, N. / Duewel, S. / Schmermund, L. / Benary, G.E. / Ranaghan, K. / Mulholland, A. / Opperman, D.J. / Hoebenreich, S.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromate reductase
B: Chromate reductase
C: Chromate reductase
D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,9288
Polymers152,1034
Non-polymers1,8254
Water5,621312
1
A: Chromate reductase
hetero molecules

A: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9644
Polymers76,0522
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4220 Å2
ΔGint-25 kcal/mol
Surface area24900 Å2
MethodPISA
2
B: Chromate reductase
hetero molecules

B: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9644
Polymers76,0522
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4250 Å2
ΔGint-28 kcal/mol
Surface area24610 Å2
MethodPISA
3
D: Chromate reductase
hetero molecules

C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9644
Polymers76,0522
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPISA
4
C: Chromate reductase
hetero molecules

D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9644
Polymers76,0522
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4270 Å2
ΔGint-26 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.680, 101.200, 104.260
Angle α, β, γ (deg.)90.000, 115.240, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Chromate reductase


Mass: 38025.766 Da / Num. of mol.: 4 / Mutation: C25D I67T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus (bacteria) / Gene: chrR / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B0JDW3
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→101.2 Å / Num. obs: 83126 / % possible obs: 99.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.063 / Rrim(I) all: 0.113 / Rsym value: 0.093 / Net I/av σ(I): 5.9 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.3-2.4230.7360.80.5080.8980.73699.7
2.42-2.5730.4611.30.3170.5610.46199.7
2.57-2.753.10.2892.20.1940.3490.28999.9
2.75-2.9730.1873.50.130.2280.18799.8
2.97-3.253.10.1165.70.0780.140.11699.9
3.25-3.643.20.0748.90.0490.0890.07499.9
3.64-4.23.10.05411.70.0370.0660.05499.9
4.2-5.143.10.05211.70.0350.0630.05299.9
5.14-7.2730.06890.0460.0830.06899.9
7.27-90.16430.04111.10.0290.0510.04199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.61 Å90.16 Å
Translation6.61 Å90.16 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HF3

3hf3


Resolution: 2.3→101.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.945 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 4084 4.9 %RANDOM
Rwork0.1819 ---
obs0.1839 79009 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.4 Å2 / Biso mean: 47.544 Å2 / Biso min: 18.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.11 Å2
2---0.19 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.3→101.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10700 0 124 312 11136
Biso mean--32.22 40.84 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911147
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210870
X-RAY DIFFRACTIONr_angle_refined_deg1.5582.00415196
X-RAY DIFFRACTIONr_angle_other_deg0.974324919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27551400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23121.787470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.014151757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.50415129
X-RAY DIFFRACTIONr_chiral_restr0.0830.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022539
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 275 -
Rwork0.295 5822 -
all-6097 -
obs--99.4 %

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