[English] 日本語
Yorodumi
- PDB-5gxu: Cystal structure of Arabidopsis ATR2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gxu
TitleCystal structure of Arabidopsis ATR2
ComponentsNADPH--cytochrome P450 reductase 2
KeywordsOXIDOREDUCTASE / NADPH-CYTOCHROME P450 REDUCTASE
Function / homology
Function and homology information


phenylpropanoid metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / chloroplast / FMN binding / NADP binding / flavin adenine dinucleotide binding / membrane => GO:0016020 / oxidoreductase activity ...phenylpropanoid metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / chloroplast / FMN binding / NADP binding / flavin adenine dinucleotide binding / membrane => GO:0016020 / oxidoreductase activity / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 ...NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NADPH--cytochrome P450 reductase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsNiu, G. / Liu, L.
CitationJournal: FEBS J. / Year: 2017
Title: Structure of the Arabidopsis thaliana NADPH-cytochrome P450 reductase 2 (ATR2) provides insight into its function
Authors: Niu, G. / Zhao, S. / Wang, L. / Dong, W. / Liu, L. / He, Y.
History
DepositionSep 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Nov 8, 2023Group: 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: NADPH--cytochrome P450 reductase 2
B: NADPH--cytochrome P450 reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,1325
Polymers143,1052
Non-polymers2,0273
Water6,756375
1
A: NADPH--cytochrome P450 reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7943
Polymers71,5521
Non-polymers1,2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area24430 Å2
MethodPISA
2
B: NADPH--cytochrome P450 reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3382
Polymers71,5521
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-9 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.333, 61.821, 88.331
Angle α, β, γ (deg.)97.840, 100.510, 90.270
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein NADPH--cytochrome P450 reductase 2 / P450R 2


Mass: 71552.453 Da / Num. of mol.: 2 / Fragment: UNP residues 73-711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SUM3, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 21% (w/v)5000 MME, 0.1M MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48501 / % possible obs: 96.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.03 / CC1/2: 0.573 / % possible all: 97.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1amo

1amo


Resolution: 2.3→30.608 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.21
RfactorNum. reflection% reflection
Rfree0.2483 2355 5.13 %
Rwork0.1996 --
obs0.2021 45927 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.99 Å2 / Biso mean: 22.24 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 2.3→30.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 137 375 7751
Biso mean--17.64 21.41 -
Num. residues----946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067597
X-RAY DIFFRACTIONf_angle_d1.01310344
X-RAY DIFFRACTIONf_chiral_restr0.0671136
X-RAY DIFFRACTIONf_plane_restr0.0041319
X-RAY DIFFRACTIONf_dihedral_angle_d15.1892728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.34690.2774860.21841781186764
2.3469-2.39790.31071090.23821992210170
2.3979-2.45370.28551030.23772135223876
2.4537-2.5150.31741380.2392398253685
2.515-2.5830.32981330.24832628276193
2.583-2.6590.3041400.24792738287897
2.659-2.74470.28341590.24612722288197
2.7447-2.84280.29471450.23692760290597
2.8428-2.95650.27481560.23422778293498
2.9565-3.09090.32071510.2312765291698
3.0909-3.25370.27941400.21592764290497
3.2537-3.45730.26691550.19772732288797
3.4573-3.72380.221700.18352672284297
3.7238-4.09780.22621330.17572716284996
4.0978-4.68890.18291440.1652715285995
4.6889-5.90060.23731430.17512672281595
5.9006-30.61040.19041500.16712604275493

+
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