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- PDB-8j43: Reductive aminase RA29-WT -

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Basic information

Entry
Database: PDB / ID: 8j43
TitleReductive aminase RA29-WT
ComponentsBeta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Reductive aminase / keto esters / oxidoreductases
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesFrankia sp. QA3 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsZheng, X.Y. / Xu, G.C. / Ni, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077054 China
CitationJournal: To Be Published
Title: Dynamic kinetic reductive resolution of cyclic keto esters by newly identified stereo complementary reductive aminases.
Authors: Zheng, X.Y. / Xu, G.C. / Ni, Y.
History
DepositionApr 19, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 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: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
B: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4006
Polymers62,7892
Non-polymers1,6114
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-96 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.521, 95.904, 67.395
Angle α, β, γ (deg.)90.00, 96.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase / RA29


Mass: 31394.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. QA3 (bacteria) / Gene: FraQA3DRAFT_3094 / Production host: Escherichia coli (E. coli) / References: UniProt: I8QLV7
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: calcium acetate trihydrate,PEG3350

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 1, 2023 / Details: multilyer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.03→42.25 Å / Num. obs: 34365 / % possible obs: 99.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.4
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 0.453 / Num. unique obs: 2238

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.592 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23751 1735 5.1 %RANDOM
Rwork0.19945 ---
obs0.2014 32600 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.518 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20.77 Å2
2---1.69 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.03→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 104 250 4552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194422
X-RAY DIFFRACTIONr_bond_other_d0.0010.024090
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9916074
X-RAY DIFFRACTIONr_angle_other_deg0.80139408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04723.457162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74115616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3681524
X-RAY DIFFRACTIONr_chiral_restr0.070.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
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_it1.0141.9852282
X-RAY DIFFRACTIONr_mcbond_other1.0121.9842281
X-RAY DIFFRACTIONr_mcangle_it1.682.9692850
X-RAY DIFFRACTIONr_mcangle_other1.682.972851
X-RAY DIFFRACTIONr_scbond_it1.3842.152140
X-RAY DIFFRACTIONr_scbond_other1.3842.152140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2223.163223
X-RAY DIFFRACTIONr_long_range_B_refined3.42824.3255109
X-RAY DIFFRACTIONr_long_range_B_other3.33424.1115019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8736 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 120 -
Rwork0.285 2113 -
obs--89.32 %

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