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- PDB-8uar: Rhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex -... -

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Basic information

Entry
Database: PDB / ID: 8uar
TitleRhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex - Compound 4b
ComponentsRhodococcus ruber ADH
KeywordsOXIDOREDUCTASE / Complex / Redox / Biomimetic
Function / homologyCITRIC ACID / ISOPROPYL ALCOHOL / :
Function and homology information
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsWilson, L.A. / Schenk, G. / Guddat, L.W. / 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 22, 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: Rhodococcus ruber ADH
B: Rhodococcus ruber ADH
C: Rhodococcus ruber ADH
D: Rhodococcus ruber ADH
E: Rhodococcus ruber ADH
F: Rhodococcus ruber ADH
G: Rhodococcus ruber ADH
H: Rhodococcus ruber ADH
I: Rhodococcus ruber ADH
J: Rhodococcus ruber ADH
K: Rhodococcus ruber ADH
L: Rhodococcus ruber ADH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,98753
Polymers448,71012
Non-polymers5,27841
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.295, 158.177, 272.938
Angle α, β, γ (deg.)90.00, 91.05, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Rhodococcus ruber ADH


Mass: 37392.473 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 70 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-W46 / 1-{[4-(hydroxymethyl)phenyl]methyl}-1,4-dihydropyridine-3-carboxamide


Mass: 244.289 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C14H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Citrate tribasic, pH 5.0, 30% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.99→49.18 Å / Num. obs: 133770 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.094 / Rrim(I) all: 0.179 / Χ2: 0.57 / Net I/σ(I): 6.2 / Num. measured all: 469362
Reflection shellResolution: 2.99→3.04 Å / % possible obs: 95.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.587 / Num. measured all: 22097 / Num. unique obs: 6345 / CC1/2: 0.737 / Rpim(I) all: 0.363 / Rrim(I) all: 0.691 / Χ2: 0.57 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→49.18 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.665 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.009 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24562 2010 1.5 %RANDOM
Rwork0.19306 ---
obs0.19384 131738 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.986 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å2-0 Å2-0.77 Å2
2---1.22 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.99→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30087 0 291 29 30407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01230996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.80142308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51554184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.3025227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.949104346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.24899
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223674
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4073.85216766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.546.9220937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2154.13414230
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.1544.4844505
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.065 Å
RfactorNum. reflection% reflection
Rfree0.33 145 -
Rwork0.308 9390 -
obs--96.97 %

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