[English] 日本語
Yorodumi
- PDB-5cpo: Crystal structure of XenA from Pseudomonas putida in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cpo
TitleCrystal structure of XenA from Pseudomonas putida in complex with an NADH mimic (mBu)
ComponentsXenobiotic reductase
KeywordsOXIDOREDUCTASE / XenA / mimic mBu
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
Chem-FNR / 1-butyl-1,4,5,6-tetrahydropyridine-3-carboxamide / Xenobiotic reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLevy, C.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes.
Authors: Knaus, T. / Paul, C.E. / Levy, C.W. / de Vries, S. / Mutti, F.G. / Hollmann, F. / Scrutton, N.S.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xenobiotic reductase
B: Xenobiotic reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2497
Polymers81,9282
Non-polymers1,3215
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-39 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.110, 84.140, 156.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#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 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R9V9
#2: Chemical ChemComp-XEN / 1-butyl-1,4,5,6-tetrahydropyridine-3-carboxamide


Mass: 182.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate buffer pH 6.5, 40% v/v PEG 300 (JCSG+ HT96 A10 Molecular Dimensions).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.65→57.38 Å / Num. obs: 91730 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1103 / Net I/σ(I): 12.48
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.618 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_1977refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H90

2h90


Resolution: 1.65→57.38 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 4506 4.91 %RAndom
Rwork0.1568 ---
obs0.1583 91681 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→57.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 89 694 6335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015858
X-RAY DIFFRACTIONf_angle_d1.2437991
X-RAY DIFFRACTIONf_dihedral_angle_d12.7532057
X-RAY DIFFRACTIONf_chiral_restr0.054835
X-RAY DIFFRACTIONf_plane_restr0.0071050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.33281360.3442895X-RAY DIFFRACTION100
1.6688-1.68840.35361510.33172867X-RAY DIFFRACTION100
1.6884-1.7090.35891370.30542846X-RAY DIFFRACTION100
1.709-1.73060.32451580.29132900X-RAY DIFFRACTION100
1.7306-1.75340.28181430.27322844X-RAY DIFFRACTION100
1.7534-1.77740.27381550.26092872X-RAY DIFFRACTION100
1.7774-1.80280.27071360.24522867X-RAY DIFFRACTION100
1.8028-1.82970.32971410.2292880X-RAY DIFFRACTION100
1.8297-1.85830.23961560.20852871X-RAY DIFFRACTION100
1.8583-1.88880.23981430.19832885X-RAY DIFFRACTION100
1.8888-1.92130.22561320.18552900X-RAY DIFFRACTION100
1.9213-1.95630.20661470.1792886X-RAY DIFFRACTION100
1.9563-1.99390.19821560.18252878X-RAY DIFFRACTION100
1.9939-2.03460.20221330.17012909X-RAY DIFFRACTION100
2.0346-2.07890.21311540.1562852X-RAY DIFFRACTION100
2.0789-2.12720.20571610.15342878X-RAY DIFFRACTION100
2.1272-2.18040.19791600.14492883X-RAY DIFFRACTION100
2.1804-2.23940.17331570.14032865X-RAY DIFFRACTION100
2.2394-2.30530.19051590.14072925X-RAY DIFFRACTION100
2.3053-2.37970.16061690.13372884X-RAY DIFFRACTION100
2.3797-2.46470.19761540.13132884X-RAY DIFFRACTION100
2.4647-2.56340.16571500.12882910X-RAY DIFFRACTION100
2.5634-2.68010.16221450.12422926X-RAY DIFFRACTION100
2.6801-2.82140.18531400.132944X-RAY DIFFRACTION100
2.8214-2.99810.16781350.14562932X-RAY DIFFRACTION100
2.9981-3.22960.1641450.15312944X-RAY DIFFRACTION100
3.2296-3.55460.16951560.14072951X-RAY DIFFRACTION100
3.5546-4.06880.15771570.12792979X-RAY DIFFRACTION100
4.0688-5.12580.13921700.12242973X-RAY DIFFRACTION100
5.1258-57.41930.17391700.16663145X-RAY DIFFRACTION100

+
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