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- PDB-7og3: IRED-88 -

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Basic information

Entry
Database: PDB / ID: 7og3
TitleIRED-88
ComponentsNAD(P)-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Imine reductase
Function / homology
Function and homology information


organic acid catabolic process / 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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesStreptomyces spectabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsFaller, M. / Koch, E.
CitationJournal: Acs Catalysis / Year: 2021
Title: Machine-Directed Evolution of an Imine Reductase for Activity and Stereoselectivity
Authors: Ma, E.J. / Siirola, E. / Moore, C. / Kummer, A. / Stoeckli, M. / Faller, M. / Bouquet, C. / Eggimann, F. / Ligibel, M. / Huynh, D. / Cutler, G. / Siegrist, L. / Lewis, R.A. / Acker, A.C. / ...Authors: Ma, E.J. / Siirola, E. / Moore, C. / Kummer, A. / Stoeckli, M. / Faller, M. / Bouquet, C. / Eggimann, F. / Ligibel, M. / Huynh, D. / Cutler, G. / Siegrist, L. / Lewis, R.A. / Acker, A.C. / Freund, E. / Koch, E. / Vogel, M. / Schlingensiepen, H. / Oakeley, E.J. / Snajdrova, R.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)-dependent oxidoreductase
B: NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5806
Polymers68,0432
Non-polymers1,5374
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-102 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.856, 75.746, 97.081
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD(P)-dependent oxidoreductase


Mass: 34021.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces spectabilis (bacteria) / Gene: CP982_37880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5P2XKZ4
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1M HEPES, 1.39M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→59.72 Å / Num. obs: 43308 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 9.44
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.286 / Num. unique obs: 4218 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGY

3zgy


Resolution: 1.904→59.72 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2225 -RANDOM
Rwork0.206 ---
obs0.2073 43308 99.9 %-
Displacement parametersBiso mean: 28.63 Å2
Baniso -1Baniso -2Baniso -3
1--6.8856 Å20 Å20 Å2
2---2.2136 Å20 Å2
3---9.0992 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.904→59.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 98 339 4684
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084457HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.886126HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1438SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes786HARMONIC5
X-RAY DIFFRACTIONt_it4457HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion593SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4357SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion13.93
LS refinement shellResolution: 1.92→1.97 Å
RfactorNum. reflection% reflection
Rfree0.3367 34 -
Rwork0.2645 --
obs--100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06710.11420.20490.34010.2120.9222-0.0465-0.0683-0.0435-0.06830.07070.071-0.04350.071-0.02420.1017-0.00490.0139-0.0842-0.0063-0.04382.973313.1788-27.4952
20.27440.26550.42870.22990.33721.03480.08660.03720.13210.0372-0.0902-0.10570.1321-0.10570.00360.0917-0.00350.003-0.0906-0.0055-0.06183.587814.88543.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A12 - 301
2X-RAY DIFFRACTION1{ A|* }A501 - 502
3X-RAY DIFFRACTION2{ B|* }B12 - 301
4X-RAY DIFFRACTION2{ B|* }B501 - 502

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