[English] 日本語
Yorodumi
- PDB-7put: Crystal structure of Thioredoxin Reductase from Brugia Malayi in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7put
TitleCrystal structure of Thioredoxin Reductase from Brugia Malayi in complex with NADP(H)
Components(Glutaredoxin domain-containing ...) x 2
KeywordsFLAVOPROTEIN / Glutaredoxin / selenocysteine / OXIDOREDUCTASE
Function / homology
Function and homology information


ecdysis, collagen and cuticulin-based cuticle / thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFata, F. / Ardini, M. / Silvestri, I. / Gabriele, F. / Ippoliti, R. / Gencheva, R. / Cheng, Q. / Arner, E.S.J. / Angelucci, F. / Williams, D.L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Redox Biol / Year: 2022
Title: Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus.
Authors: Fata, F. / Gencheva, R. / Cheng, Q. / Lullo, R. / Ardini, M. / Silvestri, I. / Gabriele, F. / Ippoliti, R. / Bulman, C.A. / Sakanari, J.A. / Williams, D.L. / Arner, E.S.J. / Angelucci, F.
History
DepositionSep 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaredoxin domain-containing protein
B: Glutaredoxin domain-containing protein
C: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,01514
Polymers198,3243
Non-polymers3,69111
Water18010
1
A: Glutaredoxin domain-containing protein
B: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,14312
Polymers132,2382
Non-polymers2,90510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-133 kcal/mol
Surface area46120 Å2
MethodPISA
2
C: Glutaredoxin domain-containing protein
hetero molecules

C: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7454
Polymers132,1742
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9630 Å2
ΔGint-68 kcal/mol
Surface area48230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.390, 260.287, 130.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Glutaredoxin domain-containing ... , 2 types, 3 molecules ABC

#1: Protein Glutaredoxin domain-containing protein / BMA-TRXR-1 / isoform d


Mass: 66118.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cysteine 345 of both chains A and B is modified into S-HYDROPEROXYCYSTEINE (PDB ID: 2CO)
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025
Production host: synthetic Escherichia coli C321.deltaA (bacteria)
Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7
#2: Protein Glutaredoxin domain-containing protein / BMA-TRXR-1 / isoform d


Mass: 66086.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025
Production host: synthetic Escherichia coli C321.deltaA (bacteria)
Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7

-
Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris/HCl pH 8, 5mM DTT, 20% MPD / PH range: 7.5-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→49.13 Å / Num. obs: 61904 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4537 / CC1/2: 0.874

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QFA_A, 4TR1

4tr1


Resolution: 2.8→49.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 27.312 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.906 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 3054 4.9 %RANDOM
Rwork0.196 ---
obs0.1975 58828 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 314.42 Å2 / Biso mean: 103.503 Å2 / Biso min: 47.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å20 Å2
2--0.77 Å2-0 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 2.8→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13176 0 246 10 13432
Biso mean--94.88 68.29 -
Num. residues----1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313691
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712920
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.64818539
X-RAY DIFFRACTIONr_angle_other_deg1.2991.57930001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67351683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98323.046627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.041152397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8151563
X-RAY DIFFRACTIONr_chiral_restr0.0730.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022729
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 245 -
Rwork0.298 4278 -
all-4523 -
obs--100 %
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)
12.1228-0.81970.09441.945-0.40311.89190.21150.25910.5238-0.0038-0.064-0.0162-0.441-0.0089-0.14750.1843-0.01840.08340.08540.05710.1974-39.7488-41.6242-17.1996
22.4199-1.35220.29272.2873-0.27541.56940.2070.0576-0.2678-0.0426-0.10630.09520.48130.4079-0.10070.33630.0373-0.09430.1484-0.0030.0535-20.9924-78.445-7.7006
35.71610.4488-2.27531.3356-0.27963.5794-0.4399-1.2018-0.08940.13110.1599-0.61240.541.50870.280.5830.3204-0.05370.8773-0.05890.7887-52.9996-120.9005-29.3811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 587
2X-RAY DIFFRACTION2B12 - 586
3X-RAY DIFFRACTION3C14 - 586

+
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