[English] 日本語
Yorodumi
- PDB-7p9e: Chlamydomonas reinhardtii NADPH Dependent Thioredoxin Reductase 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p9e
TitleChlamydomonas reinhardtii NADPH Dependent Thioredoxin Reductase 1 domain CS mutant
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / flavoprotein / FAD binding domain
Function / homology
Function and homology information


regulation of starch biosynthetic process / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / regulation of chlorophyll biosynthetic process / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / enzyme activator activity / chloroplast / hydrogen peroxide catabolic process / nucleotide binding
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin domain profile. / FAD/NAD(P)-binding domain / Thioredoxin domain ...Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin domain profile. / FAD/NAD(P)-binding domain / Thioredoxin domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Thioredoxin reductase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsFuesser, F. / Kuemmel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HI 739/14.2 Germany
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structural analysis revealed a novel conformation of the NTRC reductase domain from Chlamydomonas reinhardtii.
Authors: Marchetti, G.M. / Fusser, F. / Singh, R.K. / Brummel, M. / Koch, O. / Kummel, D. / Hippler, M.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,7896
Polymers104,8942
Non-polymers1,8964
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-24 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.149, 80.299, 95.636
Angle α, β, γ (deg.)90.000, 90.014, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-502-

P4G

21B-502-

P4G

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 101 or resid 103...
d_2ens_1(chain "B" and (resid 1 through 101 or resid 103...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLEUA1 - 101
d_12ens_1ALASERA103 - 127
d_13ens_1GLYALAA129 - 168
d_14ens_1HISMETA170 - 180
d_15ens_1ALALEUA182 - 213
d_16ens_1GLYGLNA215 - 315
d_17ens_1FADFADB
d_21ens_1METLEUC1 - 101
d_22ens_1ALASERC103 - 127
d_23ens_1GLYALAC129 - 168
d_24ens_1HISMETC170 - 180
d_25ens_1ALALEUC182 - 213
d_26ens_1GLYGLNC215 - 315
d_27ens_1FADFADD

-
Components

#1: Protein Thioredoxin reductase


Mass: 52446.910 Da / Num. of mol.: 2 / Mutation: C136S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_01g054150v5 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K3E888, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 500*MME, 10% PEG 20000, 0.1M Sodium HEPES/ MOPS (acid), 0.1M Carboxylic acids

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976244 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976244 Å / Relative weight: 1
ReflectionResolution: 2.36→49.65 Å / Num. obs: 26332 / % possible obs: 99.71 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.3
Reflection shellResolution: 2.36→2.444 Å / Num. unique obs: 2608 / CC1/2: 0.78 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P9D

7p9d


Resolution: 2.36→49.65 Å / SU ML: 0.3926 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1316 5 %
Rwork0.1782 24992 -
obs0.1816 26308 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.63 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 128 88 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795020
X-RAY DIFFRACTIONf_angle_d0.98156802
X-RAY DIFFRACTIONf_chiral_restr0.0533744
X-RAY DIFFRACTIONf_plane_restr0.0089879
X-RAY DIFFRACTIONf_dihedral_angle_d11.8628711
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.441317730128 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.450.41081420.32682702X-RAY DIFFRACTION97.06
2.45-2.560.34641450.25812743X-RAY DIFFRACTION99.76
2.56-2.70.28951470.23742783X-RAY DIFFRACTION99.56
2.7-2.870.30491450.24242756X-RAY DIFFRACTION99.86
2.87-3.090.32091470.23972789X-RAY DIFFRACTION99.83
3.09-3.40.2821470.19992794X-RAY DIFFRACTION99.83
3.4-3.890.25711470.16732795X-RAY DIFFRACTION99.9
3.89-4.90.1771470.12852790X-RAY DIFFRACTION99.8
4.9-49.650.17681490.13222840X-RAY DIFFRACTION99.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.083905846980.471425957776-0.9475950362652.01565492072-0.08562733688892.735862038320.08258639726310.0803936062191-0.0130215904733-0.096961292834-0.0445349352318-0.0676889076454-0.001500036480070.0501255370247-0.03708632535530.452334921851-0.00741297641958-0.02041845877270.375021538402-0.007060293560980.3263820252496.88236180249-11.80392297448.45250141647
20.3067724228290.1766974008380.01289210060523.96453059326-1.276386955331.186653079150.0140708617021-0.0453191959063-0.0705962211028-0.1774605567890.0286715530669-0.02374607468610.06499963817890.0418124212493-0.04730018753610.550053863590.01182860651540.0156876663180.425409240436-0.002905869073270.37492646671110.9611606181-41.152777537817.9089171193
31.987314627950.488219411347-0.2271793220831.54356408618-0.7035193488294.05929762486-0.08062644358930.1555521315260.0221226234496-0.08783074050470.0910599948904-0.1802149863770.02866376785290.4627828103850.006706872509840.330433182758-0.04383809876060.002845098388740.427290907589-0.01382844854550.34199936577419.2960110594-10.930812476412.9681227815
42.34404580822-0.9925750363211.981443721222.84557204751-1.404028701285.055640579460.00179578190827-0.06764874226260.05445735136230.0892842547143-0.0654275602292-0.1052653820540.1545663175110.1259332532430.05260863020790.420051001369-0.005685925819280.01359903363940.334139424256-0.02896121523740.2946947276056.89676825724-16.646612616639.3568121523
50.39887259972-0.1122036902460.2932238379323.69710467297-1.958674831772.132929683280.00141049998298-0.02298811740560.1167849358640.1971604447380.02599817147060.0187072938103-0.2040111043620.0810773890327-0.03450619480350.477165754862-0.0196294019845-0.01137346776540.379621829177-0.006705044542390.36908143053510.892618322213.048664903829.6805827631
61.35133881829-1.204290431470.2087528714174.41246212137-0.8136264346542.15207839511-0.0580075187675-0.01500975712390.04871516273010.1750043717020.0521563575572-0.106395637812-0.01507081443840.2927587473050.007977930186530.3218118752410.01487655979-0.009788325911020.458788997901-0.02120580944820.29615880275517.557850378-13.542858829934.4558321429
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 103 )AA1 - 1031 - 103
22chain 'A' and (resid 104 through 242 )AA104 - 242104 - 242
33chain 'A' and (resid 243 through 315 )AA243 - 315243 - 315
44chain 'B' and (resid 1 through 103 )BC1 - 1031 - 103
55chain 'B' and (resid 104 through 229 )BC104 - 229104 - 229
66chain 'B' and (resid 230 through 316 )BC230 - 316230 - 316

+
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