[English] 日本語
Yorodumi
- PDB-8a3x: Imine Reductase from Ensifer adhaerens in complex with NADP+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a3x
TitleImine Reductase from Ensifer adhaerens in complex with NADP+
ComponentsNAD_binding_2 domain-containing protein
KeywordsOXIDOREDUCTASE / Imine Reductase / IRED / NADP+ / amine
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesEnsifer adhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsGilio, A.K. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: A Reductive Aminase Switches to Imine Reductase Mode for a Bulky Amine Substrate.
Authors: Gilio, A.K. / Thorpe, T.W. / Heyam, A. / Petchey, M.R. / Pogranyi, B. / France, S.P. / Howard, R.M. / Karmilowicz, M.J. / Lewis, R. / Turner, N. / Grogan, G.
History
DepositionJun 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD_binding_2 domain-containing protein
B: NAD_binding_2 domain-containing protein
C: NAD_binding_2 domain-containing protein
D: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,55112
Polymers124,4214
Non-polymers3,1308
Water64936
1
A: NAD_binding_2 domain-containing protein
B: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7756
Polymers62,2102
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-96 kcal/mol
Surface area21260 Å2
MethodPISA
2
C: NAD_binding_2 domain-containing protein
D: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7756
Polymers62,2102
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-96 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.959, 57.535, 116.441
Angle α, β, γ (deg.)90.000, 94.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA3 - 2923 - 292
21PROPROLYSLYSBB3 - 2923 - 292
12METMETLYSLYSAA1 - 2921 - 292
22METMETLYSLYSCC1 - 2921 - 292
13METMETLYSLYSAA1 - 2921 - 292
23METMETLYSLYSDD1 - 2921 - 292
14PROPROLYSLYSBB3 - 2923 - 292
24PROPROLYSLYSCC3 - 2923 - 292
15PROPROLYSLYSBB3 - 2923 - 292
25PROPROLYSLYSDD3 - 2923 - 292
16METMETALAALACC1 - 2931 - 293
26METMETALAALADD1 - 2931 - 293

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
NAD_binding_2 domain-containing protein


Mass: 31105.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ensifer adhaerens (bacteria) / Gene: AC244_29830 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8BGL4
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 30% (w/v) PEG 2000 MME; 0.2 M KSCN; protein at 50 mg mL-1
Temp details: Grown at 6 deg C

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→58 Å / Num. obs: 38177 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.15 / Net I/σ(I): 4.4
Reflection shellResolution: 2.58→2.69 Å / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4621 / CC1/2: 0.67 / Rpim(I) all: 0.97

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCM

5ocm


Resolution: 2.58→58 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.897 / SU ML: 0.452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.714 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 1892 5 %RANDOM
Rwork0.2357 ---
obs0.238 36273 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.07 Å2 / Biso mean: 52.967 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å28.45 Å2
2---3.75 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.58→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 196 37 8757
Biso mean--49.99 33.55 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158354
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.63512182
X-RAY DIFFRACTIONr_angle_other_deg1.2581.57219086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66351174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22520.542406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.669151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3851571
X-RAY DIFFRACTIONr_chiral_restr0.0630.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022032
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86880.06
12B86880.06
21A87470.07
22C87470.07
31A87770.07
32D87770.07
41B86080.06
42C86080.06
51B86360.06
52D86360.06
61C87680.06
62D87680.06
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 135 -
Rwork0.354 2675 -
all-2810 -
obs--99.89 %

+
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