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- PDB-8uaj: Succinate Bound Crystal Structure of Thermus scotoductus SA-01 En... -

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Basic information

Entry
Database: PDB / ID: 8uaj
TitleSuccinate Bound Crystal Structure of Thermus scotoductus SA-01 Ene-reductase
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / Complex
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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / SUCCINIC ACID / NADPH dehydrogenase
Similarity search - Component
Biological speciesThermus scotoductus SA-01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWilson, L.A. / Guddat, L. / Schenk, G. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Catalysts / Year: 2024
Title: Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics
Authors: Rocha, R.A. / Wilson, L.A. / Schwartz, B.D. / Warden, A.C. / Guddat, L.W. / Speight, R.E. / Malins, L. / Schenk, G. / Scott, C.
History
DepositionSep 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH dehydrogenase
B: NADPH dehydrogenase
C: NADPH dehydrogenase
D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water14,646813
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules

C: NADPH dehydrogenase
hetero molecules

C: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area13640 Å2
ΔGint-46 kcal/mol
Surface area44940 Å2
MethodPISA
2
B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules

D: NADPH dehydrogenase
hetero molecules

D: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,08712
Polymers160,7894
Non-polymers2,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13790 Å2
ΔGint-43 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.642, 101.182, 101.182
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-550-

HOH

21C-592-

HOH

31C-708-

HOH

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Components

#1: Protein
NADPH dehydrogenase


Mass: 40197.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus SA-01 (bacteria) / Strain: ATCC 700910 / SA-01 / Gene: TSC_p800090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E8PRF1
#2: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Succinic acid, 0.1 M bicine, 30% MPEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.13→49.12 Å / Num. obs: 99650 / % possible obs: 97.9 % / Redundancy: 6.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.066 / Rrim(I) all: 0.166 / Χ2: 0.46 / Net I/σ(I): 8.6 / Num. measured all: 649720
Reflection shellResolution: 2.13→2.17 Å / % possible obs: 60.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.675 / Num. measured all: 16197 / Num. unique obs: 3013 / CC1/2: 0.732 / Rpim(I) all: 0.3 / Rrim(I) all: 0.742 / Χ2: 0.27 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→49.12 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 1994 2.01 %
Rwork0.1749 --
obs0.1753 99393 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10728 0 156 813 11697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211296
X-RAY DIFFRACTIONf_angle_d0.6215410
X-RAY DIFFRACTIONf_dihedral_angle_d7.4981630
X-RAY DIFFRACTIONf_chiral_restr0.0421686
X-RAY DIFFRACTIONf_plane_restr0.0052022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.27131250.24666332X-RAY DIFFRACTION90
2.19-2.250.24311410.19546992X-RAY DIFFRACTION100
2.25-2.320.20371480.18636954X-RAY DIFFRACTION100
2.32-2.390.20261410.17946982X-RAY DIFFRACTION100
2.39-2.480.20481460.17867010X-RAY DIFFRACTION100
2.48-2.580.21591410.17946946X-RAY DIFFRACTION100
2.58-2.70.23781430.18246986X-RAY DIFFRACTION100
2.7-2.840.21161410.18056990X-RAY DIFFRACTION100
2.84-3.020.21561460.18127017X-RAY DIFFRACTION100
3.02-3.250.19581380.17856990X-RAY DIFFRACTION100
3.25-3.570.21661440.16967009X-RAY DIFFRACTION100
3.57-4.090.16571440.15857022X-RAY DIFFRACTION100
4.09-5.150.16091460.14967050X-RAY DIFFRACTION100
5.15-49.120.18821500.18447119X-RAY DIFFRACTION99

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