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- PDB-8bj5: Imine Reductase IR007 from Amycolatopsis azurea -

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Basic information

Entry
Database: PDB / ID: 8bj5
TitleImine Reductase IR007 from Amycolatopsis azurea
ComponentsImine Reductase
KeywordsOXIDOREDUCTASE / Amine / Imine NADPH / biocatalyst
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 / 6-phosphogluconate dehydrogenase
Similarity search - Component
Biological speciesAmycolatopsis azurea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsGilio, A.K. / Steflik, J. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: Engineering of a Reductive Aminase to Enable the Synthesis of a Key Intermediate to a CDK 2/4/6 Inhibitor
Authors: Steflik, J. / Gilio, A. / Burns, M. / Grogan, G. / Kumar, R. / Lewis, R. / Martinez, C.
History
DepositionNov 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imine Reductase
B: Imine Reductase
C: Imine Reductase
D: Imine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9438
Polymers123,9694
Non-polymers2,9744
Water6,593366
1
A: Imine Reductase
B: Imine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4714
Polymers61,9842
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-98 kcal/mol
Surface area20020 Å2
MethodPISA
2
C: Imine Reductase
D: Imine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4714
Polymers61,9842
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-97 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.487, 142.332, 159.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Imine Reductase


Mass: 30992.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis azurea (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: M2QI47, EC: 1.5.1.48
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.49 M sodium phosphate; o.91 M potassium phosphate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.72→54.1 Å / Num. obs: 36218 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.12 / Net I/σ(I): 6.6
Reflection shellResolution: 2.72→2.84 Å / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4351 / CC1/2: 0.95 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIZ

6jiz


Resolution: 2.72→54.1 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.89 / SU B: 17.186 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27328 1812 5 %RANDOM
Rwork0.24688 ---
obs0.24828 34255 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.189 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--7.44 Å2-0 Å2
3----7.55 Å2
Refinement stepCycle: 1 / Resolution: 2.72→54.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8539 0 192 366 9097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168338
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.63212133
X-RAY DIFFRACTIONr_angle_other_deg1.251.57619153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62251136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19122.476420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.074151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5231550
X-RAY DIFFRACTIONr_chiral_restr0.0640.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021950
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_it2.4753.6044556
X-RAY DIFFRACTIONr_mcbond_other2.4753.6044555
X-RAY DIFFRACTIONr_mcangle_it3.9285.4035688
X-RAY DIFFRACTIONr_mcangle_other3.9285.4035689
X-RAY DIFFRACTIONr_scbond_it2.283.7364359
X-RAY DIFFRACTIONr_scbond_other2.2793.7364357
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7035.5226446
X-RAY DIFFRACTIONr_long_range_B_refined6.61642.37310071
X-RAY DIFFRACTIONr_long_range_B_other6.59942.40110044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86520.07
12B86520.07
21A87270.05
22A87270.05
31A86210.08
32C86210.08
41B86170.07
42A86170.07
51B88330.04
52C88330.04
61A86070.07
62C86070.07
LS refinement shellResolution: 2.72→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 124 -
Rwork0.313 2519 -
obs--99.74 %

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