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- PDB-7p9e: Chlamydomonas reinhardtii NADPH Dependent Thioredoxin Reductase 1... -

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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 / regulation of chlorophyll biosynthetic process / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / positive regulation of catalytic activity / enzyme activator activity / removal of superoxide radicals / cell redox homeostasis / chloroplast / hydrogen peroxide catabolic process
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. / Thioredoxin domain / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Diethylene glycol diethyl ether


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


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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