[English] 日本語
Yorodumi
- PDB-5ojl: Imine Reductase from Aspergillus terreus in complex with NADPH4 a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ojl
TitleImine Reductase from Aspergillus terreus in complex with NADPH4 and dibenz[c,e]azepine
ComponentsImine reductase
KeywordsOXIDOREDUCTASE / NADPH / imine reductase / reductive aminase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase activity / methylated histone binding / NADP binding / cytosol
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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / NADPH-dependent reductive aminase-like, C-terminal domain / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5-methyl-7~{H}-benzo[d][2]benzazepine / Chem-TXP / Uncharacterized protein
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSharma, M. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M006832/1 United Kingdom
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Biocatalytic Routes to Enantiomerically Enriched Dibenz[c,e]azepines.
Authors: France, S.P. / Aleku, G.A. / Sharma, M. / Mangas-Sanchez, J. / Howard, R.M. / Steflik, J. / Kumar, R. / Adams, R.W. / Slabu, I. / Crook, R. / Grogan, G. / Wallace, T.W. / Turner, N.J.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7113
Polymers30,7561
Non-polymers9552
Water1,874104
1
A: Imine reductase
hetero molecules

A: Imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4226
Polymers61,5122
Non-polymers1,9094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9990 Å2
ΔGint-90 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.329, 61.128, 167.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-498-

HOH

21A-504-

HOH

-
Components

#1: Protein Imine reductase


Mass: 30756.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEG_08501 / Plasmid: pETYSBLIC-3C / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CCT3
#2: Chemical ChemComp-9X5 / 5-methyl-7~{H}-benzo[d][2]benzazepine


Mass: 207.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N
#3: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-tris pH 5.5. 25% w/v PEG 3350 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.56→41.95 Å / Num. obs: 39537 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Net I/σ(I): 23.5
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1897 / CC1/2: 0.88 / Rpim(I) all: 0.41 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A9S

5a9s


Resolution: 1.56→41.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.769 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 2043 5.2 %RANDOM
Rwork0.23508 ---
obs0.23724 37441 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2--2.17 Å20 Å2
3----2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.56→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 64 104 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192114
X-RAY DIFFRACTIONr_bond_other_d0.0030.021948
X-RAY DIFFRACTIONr_angle_refined_deg2.17322890
X-RAY DIFFRACTIONr_angle_other_deg1.1633.0014491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82523.93966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28115295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.864157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212360
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5983.3861134
X-RAY DIFFRACTIONr_mcbond_other3.5943.3841133
X-RAY DIFFRACTIONr_mcangle_it4.645.061410
X-RAY DIFFRACTIONr_mcangle_other4.6385.0621411
X-RAY DIFFRACTIONr_scbond_it3.7843.731979
X-RAY DIFFRACTIONr_scbond_other3.7743.73977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0145.4961477
X-RAY DIFFRACTIONr_long_range_B_refined6.69841.8782217
X-RAY DIFFRACTIONr_long_range_B_other6.69941.8732218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 149 -
Rwork0.353 2700 -
obs--99.96 %

+
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://pdbjlvh1.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