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- PDB-8j44: Reductive Aminase RA34-WT -

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Basic information

Entry
Database: PDB / ID: 8j44
TitleReductive Aminase RA34-WT
Components6-phosphogluconate dehydrogenase NAD-binding protein
KeywordsOXIDOREDUCTASE / Reductive Aminase / keto ester / oxidoreductases
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
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 / 6-phosphogluconate dehydrogenase NAD-binding protein
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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: 6-phosphogluconate dehydrogenase NAD-binding protein
B: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0864
Polymers61,6002
Non-polymers1,4872
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, According to the results of the SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-90 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.732, 55.772, 86.053
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-phosphogluconate dehydrogenase NAD-binding protein / RA34


Mass: 30799.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494) (bacteria)
Gene: SSQG_04344 / Production host: Escherichia coli (E. coli) / References: UniProt: D9X416
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Tacsimate, MES monohydrate, PEG 4000

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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: Nov 25, 2022 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→23.25 Å / Num. obs: 30171 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rpim(I) all: 0.047 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.32 Å / Num. unique obs: 2558 / Rpim(I) all: 0.266

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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: 2.25→23.25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.759 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23015 1458 4.8 %RANDOM
Rwork0.19545 ---
obs0.19715 28701 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.1 Å2
2--0.36 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.25→23.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 96 150 4505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194441
X-RAY DIFFRACTIONr_bond_other_d0.0010.024166
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.996078
X-RAY DIFFRACTIONr_angle_other_deg0.81539584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93224.81158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1461516
X-RAY DIFFRACTIONr_chiral_restr0.070.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
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_it2.1663.0722338
X-RAY DIFFRACTIONr_mcbond_other2.1563.072337
X-RAY DIFFRACTIONr_mcangle_it3.4344.5932919
X-RAY DIFFRACTIONr_mcangle_other3.4334.5962920
X-RAY DIFFRACTIONr_scbond_it2.5713.2972103
X-RAY DIFFRACTIONr_scbond_other2.573.2972104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2284.8243160
X-RAY DIFFRACTIONr_long_range_B_refined5.88436.9154965
X-RAY DIFFRACTIONr_long_range_B_other5.87436.8554937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8570 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 100 -
Rwork0.258 1874 -
obs--89.04 %

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