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- PDB-8u07: Imine reductase RedE bound with NADP+ and arcyriaflavin A (second... -

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Basic information

Entry
Database: PDB / ID: 8u07
TitleImine reductase RedE bound with NADP+ and arcyriaflavin A (secondary site)
ComponentsRedE
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
: / IODIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / RedE
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RedE
B: RedE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,97025
Polymers65,4042
Non-polymers3,56623
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-187 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.588, 111.529, 67.695
Angle α, β, γ (deg.)90.000, 108.467, 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 , 1 types, 2 molecules AB

#1: Protein RedE


Mass: 32701.840 Da / Num. of mol.: 2
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 , 8 types, 609 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A7F / Arcyriaflavin A / 12,13-dihydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5,7(6H)-dione


Mass: 325.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.33 M NaI, 0.1 M Tris-HCl pH 8.5, 21 % PEG 3350, 1.5 mM TCEP
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: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.63→37.94 Å / Num. obs: 93667 / % possible obs: 98.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 0.91 / Net I/σ(I): 12.8
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5126 / CC1/2: 0.948 / Rpim(I) all: 0.276 / Rrim(I) all: 0.722 / Χ2: 0.77 / % possible all: 97.9

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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: 1.63→36.6 Å / SU ML: 0.2216 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 1708 1.83 %
Rwork0.1937 91740 -
obs0.1942 93448 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.41 Å2
Refinement stepCycle: LAST / Resolution: 1.63→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 178 586 4827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524411
X-RAY DIFFRACTIONf_angle_d0.74316073
X-RAY DIFFRACTIONf_chiral_restr0.0446684
X-RAY DIFFRACTIONf_plane_restr0.006750
X-RAY DIFFRACTIONf_dihedral_angle_d11.99761410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.391410.33847547X-RAY DIFFRACTION97.05
1.68-1.740.35711400.28767464X-RAY DIFFRACTION96.57
1.74-1.80.25281430.22737693X-RAY DIFFRACTION99.37
1.8-1.870.22191430.20567647X-RAY DIFFRACTION99
1.87-1.960.2281420.19467624X-RAY DIFFRACTION98.4
1.96-2.060.24741370.20617452X-RAY DIFFRACTION96.32
2.06-2.190.25081440.19657733X-RAY DIFFRACTION99.51
2.19-2.360.22291440.18777695X-RAY DIFFRACTION99.5
2.36-2.590.23031420.19267658X-RAY DIFFRACTION98.31
2.59-2.970.22581430.19197684X-RAY DIFFRACTION99.37
2.97-3.740.19111440.18347745X-RAY DIFFRACTION99.31
3.74-36.60.21450.17937798X-RAY DIFFRACTION99.06
Refinement TLS params.

Method: refined / 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)
10.0231000192915-0.00618730599755-0.05161249324290.2048063275570.03429725757190.05923261701520.0365682866669-0.0812749655923-0.1530626906180.04097956698680.08191967191330.1721033721950.208817459045-0.1161095518899.88071827313E-80.340569871056-0.00366125613186-0.02973938432420.2115630024680.02489309156470.27584175028710.322205749-36.5448303122-12.7786382832
20.2635937022420.0462644147955-0.03569623955140.478702147852-0.1270040037590.08145855090860.0885152317291-0.0638957537459-0.05034452943010.06289464390570.04334322655770.03977385624250.092621901283-0.0167006640449-7.9442001976E-90.228494683596-0.00563335552965-0.008292813779540.2148224793860.008081513278760.20615866759511.2050619258-22.256900208-11.7775431541
30.269676143586-0.1229034479610.2576601097350.318628926014-0.2131973368520.899009823576-0.0304582762029-0.00878148271422-0.005340826490470.02340868450120.06166553382410.0306003528941-0.0705385798462-0.0882672994354-4.7776680355E-100.1898572820360.004450122006170.009513858266030.2009322358520.007402822958160.2165984720521.44917293928-7.15649910895-36.4409488418
40.2180244439320.05167074070760.2105014996370.390575951683-0.1515652498580.392202129816-0.09565126838610.1095110154040.0802980200955-0.08314566298670.05258732944810.105940568324-0.3537771617460.152652968318-0.003955468526520.245716210983-0.05653707571670.01533189532380.258342192569-0.002237295632780.188779668635-1.33828983821-2.73299518331-69.7090609672
50.0762690983280.00590733675052-0.06858091601270.01347868356850.008372976045870.04241239304330.0980344021367-0.00135357531341-0.209421376731-0.08791446439540.0828666961713-0.121045559324-0.03381655317890.2120771949311.27880797425E-50.222698950379-0.0240120356638-0.01154895750930.361052001956-0.06672075037710.2605038165615.78320199286-8.49092993899-55.7156028794
60.49000548604-0.009583687222440.4989923504340.181849449942-0.4726957376670.7313542421970.0767657525612-0.0777990275464-0.09022102233250.007656451843880.0774375072420.01616355938170.0105053135951-0.133773951920.04359076124870.181021057988-0.009868808292310.008430293865950.2153723422190.02041204484970.222438413597-3.70759644493-14.2040977181-35.751488338
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 68 )AA3 - 681 - 66
22chain 'A' and (resid 69 through 137 )AA69 - 13767 - 135
33chain 'A' and (resid 138 through 289 )AA138 - 289136 - 287
44chain 'B' and (resid 2 through 118 )BC2 - 1181 - 106
55chain 'B' and (resid 119 through 137 )BC119 - 137107 - 125
66chain 'B' and (resid 138 through 289 )BC138 - 289126 - 277

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