[English] 日本語
Yorodumi
- PDB-8u06: Imine reductase RedE bound with NADP+ and arcyriaflavin A (primar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u06
TitleImine reductase RedE bound with NADP+ and arcyriaflavin A (primary 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: 1.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RedE
B: RedE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,81133
Polymers65,4042
Non-polymers4,40731
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15350 Å2
ΔGint-150 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.114, 110.767, 66.987
Angle α, β, γ (deg.)90.000, 107.598, 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

-
Components

-
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

-
Non-polymers , 7 types, 793 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.96 %
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, 1.5 mM TCEP
Temp details: ambient

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→37.75 Å / Num. obs: 95462 / % possible obs: 96.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 17.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 0.98 / Net I/σ(I): 14.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4628 / CC1/2: 0.845 / Rpim(I) all: 0.355 / Rrim(I) all: 0.957 / Χ2: 0.87

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→37.75 Å / SU ML: 0.1619 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 2000 2.1 %
Rwork0.1552 93375 -
obs0.1559 95375 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 202 762 5157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01024518
X-RAY DIFFRACTIONf_angle_d1.27226199
X-RAY DIFFRACTIONf_chiral_restr0.0716702
X-RAY DIFFRACTIONf_plane_restr0.0105778
X-RAY DIFFRACTIONf_dihedral_angle_d12.00541488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26821410.25746590X-RAY DIFFRACTION95.19
1.64-1.680.23351410.22546570X-RAY DIFFRACTION95.86
1.68-1.730.23761410.20746579X-RAY DIFFRACTION95.82
1.73-1.790.24471420.20456615X-RAY DIFFRACTION95.76
1.79-1.850.2291380.19266434X-RAY DIFFRACTION92.88
1.85-1.930.17711440.1646707X-RAY DIFFRACTION97.19
1.93-2.020.17661430.15686713X-RAY DIFFRACTION97.04
2.02-2.120.19541430.16036674X-RAY DIFFRACTION97
2.12-2.250.19741410.14976590X-RAY DIFFRACTION95.06
2.26-2.430.20811440.14686723X-RAY DIFFRACTION97.81
2.43-2.670.16231450.15366790X-RAY DIFFRACTION97.92
2.67-3.060.18451430.15176696X-RAY DIFFRACTION96.6
3.06-3.850.17941480.13726858X-RAY DIFFRACTION98.56
3.85-37.750.17181460.13826836X-RAY DIFFRACTION97.42
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)
10.3154328397510.1871366429560.103150985450.707377984879-0.1011325910660.4723305340180.022299697208-0.0233493048792-0.03097861400210.003154006417750.00726493702017-0.02366636986250.06671655200750.02290598663-3.93242851772E-90.196593924107-0.00657294568778-0.01586885916430.1481143834570.0009450383204220.16452956007911.2058203396-27.8169694242-13.2234996035
20.0796465979091-0.1555854824610.1504743466610.350937526069-0.3426966762470.3268837396330.01675338504110.00687137235697-0.08019545422190.00459814164480.06432496915980.009164268162150.0367247998848-0.04503922635580.0005576275761450.15936927059-0.0256823669830.0005553155549110.1679255667110.002779514362220.165953112422-0.87327584586-12.426461222-38.1288162128
30.1278336949540.01470686025860.08184405510230.418888305183-0.2077979289920.164894301190.0281531907605-0.01905568830960.0015884418990.01815578358240.007162531370880.046833006791-0.183888437851-0.07018174320810.001588179122610.1952270391040.00444065986685-0.003784582250110.1602521961770.007721853689590.166090182574-3.605588415693.05645659715-38.9385387908
40.2671286401510.2371009232040.007430272071640.323804617095-0.1791750462650.355796509444-0.08453025621750.03710925350280.0731038036685-0.1079481660450.0006185260472530.0505118786586-0.1774524159640.223716231046-0.0007897554093440.24780045006-0.0425473230507-0.008956315588070.2338036515670.001933267238240.1949659285914.078579132240.13200629242-69.8408640448
50.189205661810.217279629839-0.008809966395620.2857307357650.06378249172090.1332177231050.0185335517065-0.0327504356844-0.0415695746648-0.04248567818590.01067538107450.00775735011421-0.0564696547658-0.02274942060152.22389242565E-80.195891354105-0.00925666078609-0.0149238280.185777231318-0.01045218555070.1588801943-4.85415770929-7.57088811449-63.813659406
60.201151045153-0.07204751557220.216057615280.190443759739-0.3519993627860.6317176627090.0483535361605-0.0377895094034-0.04679065546840.007124977861330.046746152110.01107317639050.0331622155131-0.09066102661670.006961660871120.162795290896-0.03228025101630.001306824712090.1655081584660.01617706330090.165240871336-4.11427738971-14.1146527821-35.2669096659
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 160 )AA2 - 1601 - 159
22chain 'A' and (resid 161 through 227 )AA161 - 227160 - 226
33chain 'A' and (resid 228 through 290 )AA228 - 290227 - 289
44chain 'B' and (resid 0 through 79 )BB0 - 791 - 80
55chain 'B' and (resid 80 through 137 )BB80 - 13781 - 138
66chain 'B' and (resid 138 through 289 )BB138 - 289139 - 290

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more