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- PDB-5ogt: Thermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I... -

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Basic information

Entry
Database: PDB / ID: 5ogt
TitleThermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I67T_A102H
ComponentsChromate reductase
KeywordsOXIDOREDUCTASE / Ene-reductase Old yellow enzyme C25D_I67T_A102H
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 / NADPH dehydrogenase
Similarity search - Component
Biological speciesThermus scotoductus SA-01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOpperman, D.J. / Hoebenreich, S. / Nett, N.
CitationJournal: To Be Published
Title: Thermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I67T_A102H
Authors: Opperman, D.J. / Hoebenreich, S. / Nett, N.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)154,1978
Polymers152,3714
Non-polymers1,8254
Water9,350519
1
A: Chromate reductase
hetero molecules

A: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0984
Polymers76,1862
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_759-x+2,y,-z+41
2
B: Chromate reductase
hetero molecules

C: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0984
Polymers76,1862
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_759-x+2,y,-z+41
3
C: Chromate reductase
hetero molecules

B: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0984
Polymers76,1862
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_759-x+2,y,-z+41
4
D: Chromate reductase
hetero molecules

D: Chromate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0984
Polymers76,1862
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_759-x+2,y,-z+41
Unit cell
Length a, b, c (Å)100.270, 103.240, 102.720
Angle α, β, γ (deg.)90.000, 113.280, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Chromate reductase / Ene-reductase TsER


Mass: 38092.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus SA-01 (bacteria) / Gene: chrR / Plasmid: pET22-b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: B0JDW3, UniProt: E8PRF1*PLUS
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 519 / 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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.3→69.65 Å / Num. obs: 85031 / % possible obs: 99.5 % / Redundancy: 2.9 % / CC1/2: 0.92 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.127 / Rrim(I) all: 0.225 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.342.80.6680.540.470.8299.3
12.17-69.653.30.1070.9770.0660.12699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.1data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUX

5nux


Resolution: 2.3→69.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.594 / SU ML: 0.182 / SU R Cruickshank DPI: 0.2721 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.215
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 4142 4.9 %RANDOM
Rwork0.2042 ---
obs0.2061 80888 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 22.044 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0 Å20.64 Å2
2---0.41 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2.3→69.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10720 0 124 519 11363
Biso mean--13.03 26.49 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911164
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210868
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.00315216
X-RAY DIFFRACTIONr_angle_other_deg0.973324912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06551396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70221.78472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.838151756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6915128
X-RAY DIFFRACTIONr_chiral_restr0.0690.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022552
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 301 -
Rwork0.271 5923 -
all-6224 -
obs--99.09 %

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