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- PDB-8u04: Reductasporine biosynthetic pathway imine reductase RedE, apo -

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Basic information

Entry
Database: PDB / ID: 8u04
TitleReductasporine biosynthetic pathway imine reductase RedE, apo
Components(RedE) x 2
KeywordsBIOSYNTHETIC PROTEIN / indolocarbazole / imine reductase / NADPH-dependent
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
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDaniel-Ivad, P. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: An imine reductase that captures reactive intermediates in the biosynthesis of the indolocarbazole reductasporine.
Authors: Daniel-Ivad, P. / Ryan, K.S.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RedE
B: RedE
C: RedE
D: RedE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,31117
Polymers131,0364
Non-polymers1,27613
Water20,7171150
1
A: RedE
D: RedE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1209
Polymers65,4802
Non-polymers6417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RedE
C: RedE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1918
Polymers65,5562
Non-polymers6356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.780, 186.720, 71.690
Angle α, β, γ (deg.)90.000, 111.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein RedE


Mass: 32777.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: environmental DNA from soil
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: redE / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7G0Y4
#2: Protein RedE


Mass: 32701.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: environmental DNA from soil
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: redE / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7G0Y4

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Non-polymers , 5 types, 1163 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.35 M NaI, 0.1 M Bicine pH 9, 25 % PEG 3350, 5 mM beta-mercaptoethanol
Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.62→93.36 Å / Num. obs: 154438 / % possible obs: 96.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 11.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7659 / CC1/2: 0.448 / Rpim(I) all: 0.593 / Rrim(I) all: 1.546

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→93.36 Å / Cross valid method: FREE R-VALUE / σ(F): 22.47 / Phase error: 21.5898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 7991 5.18 %
Rwork0.1635 146383 -
obs0.1715 154374 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.52 Å2
Refinement stepCycle: LAST / Resolution: 1.62→93.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8280 0 33 1150 9463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00258481
X-RAY DIFFRACTIONf_angle_d0.515911582
X-RAY DIFFRACTIONf_chiral_restr0.03821354
X-RAY DIFFRACTIONf_plane_restr0.00441495
X-RAY DIFFRACTIONf_dihedral_angle_d12.1032821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.27934080.2767319X-RAY DIFFRACTION92.41
1.65-1.680.29333950.27177445X-RAY DIFFRACTION92.11
1.68-1.710.27583530.26037467X-RAY DIFFRACTION92.93
1.71-1.740.2713990.24827358X-RAY DIFFRACTION91.91
1.74-1.780.25384010.24137269X-RAY DIFFRACTION90.84
1.78-1.820.2793540.22646978X-RAY DIFFRACTION87.4
1.82-1.870.26753960.21947385X-RAY DIFFRACTION92.29
1.87-1.920.22813920.217422X-RAY DIFFRACTION92.24
1.92-1.980.22023660.20297438X-RAY DIFFRACTION92.96
1.98-2.040.22093870.2027336X-RAY DIFFRACTION91.33
2.04-2.110.24623660.19797353X-RAY DIFFRACTION91.32
2.11-2.20.24183640.1886908X-RAY DIFFRACTION86.53
2.2-2.30.21413890.18227413X-RAY DIFFRACTION92.18
2.3-2.420.1883660.17047433X-RAY DIFFRACTION92.88
2.42-2.570.20963880.177527X-RAY DIFFRACTION93.1
2.57-2.770.19423740.16287174X-RAY DIFFRACTION89.32
2.77-3.050.21134240.15687286X-RAY DIFFRACTION90.94
3.05-3.490.21663890.15717514X-RAY DIFFRACTION93.54
3.49-4.390.18193800.12247203X-RAY DIFFRACTION89.28
4.4-93.360.18723970.1317458X-RAY DIFFRACTION91.82

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