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- PDB-8u05: Reductasporine biosynthetic pathway imine reductase RedE bound wi... -

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Basic information

Entry
Database: PDB / ID: 8u05
TitleReductasporine biosynthetic pathway imine reductase RedE bound with NADP+
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
BETA-MERCAPTOETHANOL / IODIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / RedE
Similarity search - Component
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 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 2.0Mar 12, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conf / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conf.end_auth_comp_id / _struct_conf.end_label_comp_id

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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)68,14619
Polymers65,5562
Non-polymers2,59017
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-131 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.740, 111.310, 72.040
Angle α, β, γ (deg.)90.000, 107.040, 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: 32777.957 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 , 7 types, 722 molecules

#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IOD / IODIDE ION


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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.62 Å3/Da / Density % sol: 53.09 %
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, 23 % 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→68.88 Å / Num. obs: 75988 / % possible obs: 88.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Net I/σ(I): 12.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4141 / CC1/2: 0.945 / Rpim(I) all: 0.172 / Rrim(I) all: 0.449

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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→43.29 Å / SU ML: 0.172 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 3872 5.1 %
Rwork0.1716 72027 -
obs0.1733 75899 88.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.89 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 139 705 4996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534385
X-RAY DIFFRACTIONf_angle_d0.85245998
X-RAY DIFFRACTIONf_chiral_restr0.0476695
X-RAY DIFFRACTIONf_plane_restr0.007760
X-RAY DIFFRACTIONf_dihedral_angle_d11.85011440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.28791510.22682816X-RAY DIFFRACTION97.82
1.64-1.660.27381390.21052877X-RAY DIFFRACTION97.73
1.66-1.680.27041290.19962794X-RAY DIFFRACTION97.5
1.68-1.70.27461310.1962844X-RAY DIFFRACTION97.48
1.7-1.730.24111480.19062819X-RAY DIFFRACTION97.34
1.73-1.750.25191530.18112772X-RAY DIFFRACTION97.24
1.75-1.780.20651470.17962831X-RAY DIFFRACTION96.03
1.78-1.810.22991510.17832646X-RAY DIFFRACTION92.4
1.81-1.840.25331440.18422771X-RAY DIFFRACTION95.79
1.84-1.880.25131740.18642816X-RAY DIFFRACTION98
1.88-1.910.2584880.18751614X-RAY DIFFRACTION55.77
1.91-1.950.2516770.19461240X-RAY DIFFRACTION45.62
1.96-1.990.21831100.17871884X-RAY DIFFRACTION97.55
1.99-2.040.21821490.17342851X-RAY DIFFRACTION96.87
2.04-2.090.2212950.18781898X-RAY DIFFRACTION66.28
2.09-2.150.2081370.17042789X-RAY DIFFRACTION94.54
2.15-2.210.19461580.16272641X-RAY DIFFRACTION92.22
2.21-2.280.19371180.17061898X-RAY DIFFRACTION66.78
2.28-2.360.19411880.15682849X-RAY DIFFRACTION97.84
2.36-2.460.1731610.15992826X-RAY DIFFRACTION98.03
2.46-2.570.2161380.16652846X-RAY DIFFRACTION98.13
2.57-2.710.17831410.17162392X-RAY DIFFRACTION82.86
2.71-2.870.21091480.1762674X-RAY DIFFRACTION92.22
2.87-3.10.21511550.18012878X-RAY DIFFRACTION99.05
3.1-3.410.20321350.1732899X-RAY DIFFRACTION98.38
3.41-3.890.19241450.1562331X-RAY DIFFRACTION81.88
3.93-4.910.16591140.14672673X-RAY DIFFRACTION94.09
4.91-43.290.18121480.17722858X-RAY DIFFRACTION96.47
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)
10.2755918103980.09932375205930.01543240509020.7448834994610.1913664413690.4370691126020.0156263180061-0.02517065576070.03833105538680.08402971003930.0335258659674-0.113143838289-0.0867972236580.01647748241040.006087463891520.1238852350490.012408804749-0.008312679739490.101317354903-0.004627251471240.1151239886683.4992787974229.885673081321.7838331156
20.0921491431728-0.01890127584290.08458979118050.09009905703940.05051481725370.095613538856-0.04712114108990.03931585506760.0599755480975-0.2367948594750.1084082080330.0312226944147-0.061484879491-0.08703277731040.02876321490760.17389992815-0.01301151305870.03246921878370.112137525387-0.006818248871310.1127466943642.8270819286625.46398082456.46688802159
30.0256153393992-0.383412086571-0.1183552218670.1325622807880.6351926961970.5017800844230.0445254857121-0.005051778333230.0388950369846-0.00819709257460.0236552285449-0.0445693747135-0.1068083012070.0166360935819.37729235559E-60.115893883638-0.0115774554040.01120259690590.1071938196270.002551956870070.1055964227645.4236929520815.2825755087-3.11382809445
40.138799252377-0.105112963308-0.03480819197310.495347142070.3589921873840.5944374118730.08790289914390.0836895903957-0.0106329212139-0.02502568529520.0536440656085-0.05818121601020.1186643177710.07422876075910.2076770265960.1127080728670.01245053249960.005715309120970.119795416097-0.0167725329910.11891227851812.3654466975-2.49054105215-9.77612219653
50.3168185237610.297864366476-0.1273383353960.3885256479160.1867408003860.40498003265-0.102197284326-0.00643141649508-0.0408856237841-0.02360492723160.01134785550730.1386354532270.13613388295-0.179064390362-0.1253543922810.1277509166560.00108671599833-0.02529792643380.1523330042750.03685170589410.183338316008-3.18252487101-0.286812049352-38.0020863144
60.5475593014860.6652214754040.104743386730.65789521185-0.2086631588830.2865000793630.0398481535589-0.06058383981520.0423413649053-0.1100366221520.0065987502122-0.00140682635219-0.05138332474740.04323345585070.005907648568860.1190715350370.02902570950350.005661784987560.1179687383310.02346723346250.110307278697.650893433738.59998695508-34.5543187434
70.18960348776-0.211551683446-0.1273541028760.2083111942060.2853768263320.4239043744970.0535859122510.003075617226150.02770476643820.004213568587770.0177837934008-0.010021833933-0.01623510401910.01943179778220.007211347068730.114086033842-0.01153137932040.001465407259610.109712254595-0.001552407330370.09965155534948.3946817286912.7083397448-5.39306130748
80.2137004612480.0816176723189-0.1344608301350.2739720289670.3118921567130.4553207879230.0824156334496-0.1358167288680.07993608749630.1330196374570.108881174794-0.176361445187-0.1040830387080.3064528304560.129713379920.15221259989-0.0402122957859-0.0006315245731260.233754460209-0.06247708792640.19869566935522.022125510216.64866358831.06224029695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 118 )AA2 - 1181 - 117
22chain 'A' and (resid 119 through 137 )AA119 - 137118 - 136
33chain 'A' and (resid 138 through 227 )AA138 - 227137 - 226
44chain 'A' and (resid 228 through 289 )AA228 - 289227 - 288
55chain 'B' and (resid 1 through 68 )BE1 - 682 - 69
66chain 'B' and (resid 69 through 160 )BE69 - 16070 - 161
77chain 'B' and (resid 161 through 227 )BE161 - 227162 - 228
88chain 'B' and (resid 228 through 289 )BE228 - 289229 - 290

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