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- PDB-8bk1: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A... -

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Basic information

Entry
Database: PDB / ID: 8bk1
TitleMutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
ComponentsMutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
KeywordsOXIDOREDUCTASE / Amine / Imine NADPH / biocatalyst
Function / homology3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase, putative
Function and homology information
Biological speciesAmycolatopsis azurea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGilio, A.K. / Grogan, G.J.
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 8, 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: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
B: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
C: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
D: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,39416
Polymers123,6524
Non-polymers3,74212
Water4,179232
1
A: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
B: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7939
Polymers61,8262
Non-polymers1,9677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-138 kcal/mol
Surface area21070 Å2
MethodPISA
2
C: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules

C: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6978
Polymers61,8262
Non-polymers1,8716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area12350 Å2
ΔGint-125 kcal/mol
Surface area20950 Å2
MethodPISA
3
D: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules

D: Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5056
Polymers61,8262
Non-polymers1,6794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area12070 Å2
ΔGint-105 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.027, 186.027, 373.436
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-444-

HOH

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
Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L


Mass: 30913.084 Da / Num. of mol.: 4 / Mutation: E120A, M197W, M206S, A213P, D238G, I240L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis azurea (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: M2QI47
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 5.03 Å3/Da / Density % sol: 75.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bistris, 0.1 M NaCl, 1.5 M ammonium sulfate, 6% 1,4-butanediol

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→62.32 Å / Num. obs: 68344 / % possible obs: 100 % / Redundancy: 21.4 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.05 / Net I/σ(I): 14.8
Reflection shellResolution: 2.7→2.76 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4549 / CC1/2: 0.86 / Rpim(I) all: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIZ

6jiz


Resolution: 2.7→62.32 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.934 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21087 3394 5 %RANDOM
Rwork0.1882 ---
obs0.18932 64923 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.075 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 2.7→62.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8554 0 232 232 9018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139048
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158374
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.63212341
X-RAY DIFFRACTIONr_angle_other_deg1.3931.57619210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77751159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47721.906425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.649151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1161556
X-RAY DIFFRACTIONr_chiral_restr0.0840.21183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022022
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_it6.0646.3334630
X-RAY DIFFRACTIONr_mcbond_other6.0416.3324629
X-RAY DIFFRACTIONr_mcangle_it8.3859.4855788
X-RAY DIFFRACTIONr_mcangle_other8.3859.4865789
X-RAY DIFFRACTIONr_scbond_it6.5966.6074417
X-RAY DIFFRACTIONr_scbond_other6.5636.5944407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3039.7316541
X-RAY DIFFRACTIONr_long_range_B_refined11.04273.2069819
X-RAY DIFFRACTIONr_long_range_B_other11.04473.2059804
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)
11A88150.07
12B88150.07
21A86610.06
22D86610.06
31A85000.08
32C85000.08
41B86910.07
42D86910.07
51B84480.09
52C84480.09
61D84850.07
62C84850.07
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 245 -
Rwork0.285 4769 -
obs--99.88 %

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