[English] 日本語
Yorodumi
- PDB-8a8i: Xenobiotic reductase A from Pseudomonas putida in complex with et... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a8i
TitleXenobiotic reductase A from Pseudomonas putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
ComponentsXenobiotic reductase
KeywordsOXIDOREDUCTASE / Ene-reductase / complex / oxime / FMN
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding / metal ion binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-L9I / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Acs Catalysis / Year: 2023
Title: Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.
Authors: Breukelaar, W.B. / Polidori, N. / Singh, A. / Daniel, B. / Glueck, S.M. / Gruber, K. / Kroutil, W.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 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
B: Xenobiotic reductase
D: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,55710
Polymers81,9282
Non-polymers1,6298
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-34 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.149, 158.863, 49.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTYRTYR(chain 'B' and (resid 2 through 8 or resid 10...BA2 - 82 - 8
12LEULEUASNASN(chain 'B' and (resid 2 through 8 or resid 10...BA10 - 3510 - 35
13TRPTRPASNASN(chain 'B' and (resid 2 through 8 or resid 10...BA37 - 11037 - 110
14PROPROASPASP(chain 'B' and (resid 2 through 8 or resid 10...BA112 - 123112 - 123
15GLYGLYPROPRO(chain 'B' and (resid 2 through 8 or resid 10...BA126 - 145126 - 145
16ALAALAILEILE(chain 'B' and (resid 2 through 8 or resid 10...BA147 - 153147 - 153
17VALVALARGARG(chain 'B' and (resid 2 through 8 or resid 10...BA156 - 209156 - 209
18LEULEUVALVAL(chain 'B' and (resid 2 through 8 or resid 10...BA211 - 218211 - 218
19VALVALPROPRO(chain 'B' and (resid 2 through 8 or resid 10...BA221 - 223221 - 223
110ASNASNGLUGLU(chain 'B' and (resid 2 through 8 or resid 10...BA225 - 242225 - 242
111THRTHRTHRTHR(chain 'B' and (resid 2 through 8 or resid 10...BA244244
112GLUGLUPROPRO(chain 'B' and (resid 2 through 8 or resid 10...BA246 - 307246 - 307
113LEULEULEULEU(chain 'B' and (resid 2 through 8 or resid 10...BA309 - 314309 - 314
114ALAALAGLUGLU(chain 'B' and (resid 2 through 8 or resid 10...BA316 - 360316 - 360
21SERSERTYRTYR(chain 'D' and (resid 2 through 8 or resid 10...DB2 - 82 - 8
22LEULEUASNASN(chain 'D' and (resid 2 through 8 or resid 10...DB10 - 3510 - 35
23TRPTRPASNASN(chain 'D' and (resid 2 through 8 or resid 10...DB37 - 11037 - 110
24PROPROASPASP(chain 'D' and (resid 2 through 8 or resid 10...DB112 - 123112 - 123
25GLYGLYPROPRO(chain 'D' and (resid 2 through 8 or resid 10...DB126 - 145126 - 145
26ALAALAILEILE(chain 'D' and (resid 2 through 8 or resid 10...DB147 - 153147 - 153
27VALVALARGARG(chain 'D' and (resid 2 through 8 or resid 10...DB156 - 209156 - 209
28LEULEUVALVAL(chain 'D' and (resid 2 through 8 or resid 10...DB211 - 218211 - 218
29VALVALPROPRO(chain 'D' and (resid 2 through 8 or resid 10...DB221 - 223221 - 223
210ASNASNGLUGLU(chain 'D' and (resid 2 through 8 or resid 10...DB225 - 242225 - 242
211THRTHRTHRTHR(chain 'D' and (resid 2 through 8 or resid 10...DB244244
212GLUGLUPROPRO(chain 'D' and (resid 2 through 8 or resid 10...DB246 - 307246 - 307
213LEULEULEULEU(chain 'D' and (resid 2 through 8 or resid 10...DB309 - 314309 - 314
214ALAALAGLUGLU(chain 'D' and (resid 2 through 8 or resid 10...DB316 - 360316 - 360

-
Components

-
Protein , 1 types, 2 molecules BD

#1: Protein Xenobiotic reductase / Xenobiotic reductase A


Mass: 40964.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xenA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R9V9

-
Non-polymers , 6 types, 588 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-L9I / ethyl (2Z)-2-hydroxyimino-3-oxidanylidene-butanoate


Mass: 159.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: 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
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM halogen mix (30 mM NaF, 30 mM NaBr, 30 mM NaI), 5% MPD, 25% PEG 3350, 100 mM Tris pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.88→44.67 Å / Num. obs: 99224 / % possible obs: 94.33 % / Redundancy: 2.6 % / Biso Wilson estimate: 18.18 Å2 / CC1/2: 0.951 / Net I/σ(I): 3.64
Reflection shellResolution: 1.88→1.947 Å / Num. unique obs: 8305 / CC1/2: 0.704

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n19

3n19


Resolution: 1.88→44.67 Å / SU ML: 0.3017 / Cross valid method: FREE R-VALUE / σ(F): 0.56 / Phase error: 24.8511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1440 1.48 %
Rwork0.1838 96114 -
obs0.1846 97554 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.65 Å2
Refinement stepCycle: LAST / Resolution: 1.88→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 109 580 6241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675973
X-RAY DIFFRACTIONf_angle_d0.88368165
X-RAY DIFFRACTIONf_chiral_restr0.0533849
X-RAY DIFFRACTIONf_plane_restr0.00621083
X-RAY DIFFRACTIONf_dihedral_angle_d13.70942105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.950.44661250.45698087X-RAY DIFFRACTION79.72
1.95-2.030.27231530.256910040X-RAY DIFFRACTION98.38
2.03-2.120.32611380.24839343X-RAY DIFFRACTION91.73
2.12-2.230.27631470.21029675X-RAY DIFFRACTION94.74
2.23-2.370.27171410.20869465X-RAY DIFFRACTION92.47
2.37-2.550.2381440.16479950X-RAY DIFFRACTION98.15
2.55-2.810.22291510.16889711X-RAY DIFFRACTION95.41
2.81-3.210.18851460.14789980X-RAY DIFFRACTION97.81
3.21-4.050.21591460.14829766X-RAY DIFFRACTION95.7
4.05-44.670.19571490.148210097X-RAY DIFFRACTION99.15

+
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