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- PDB-5g30: Crystallographic structure of mutant D60S of thioredoxin from Lit... -

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Basic information

Entry
Database: PDB / ID: 5g30
TitleCrystallographic structure of mutant D60S of thioredoxin from Litopenaeus vannamei
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMEI / MUTANT / DISULFIDE BOND
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Thioredoxin
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCampos-Acevedo, A.A. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.
Authors: Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Perez, J. / Rudino-Pinera, E.
History
DepositionApr 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1129
Polymers47,7234
Non-polymers3895
Water7,044391
1
B: THIOREDOXIN
C: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1926
Polymers23,8612
Non-polymers3304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-3.8 kcal/mol
Surface area10930 Å2
MethodPISA
2
A: THIOREDOXIN
D: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9203
Polymers23,8612
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-6.7 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.491, 82.712, 82.206
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
THIOREDOXIN


Mass: 11930.700 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11.
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1PWB9, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENILALANINE

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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: 2.02 Å3/Da / Density % sol: 39.17 % / Description: NONE
Crystal growpH: 6
Details: 10 % (W/V) POLYETHYLENE GLYCOL 8,000. 100 MM MES PH 6.0. 200 MM ZINC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→19.46 Å / Num. obs: 45126 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZX

3zzx


Resolution: 1.65→19.465 Å / SU ML: 0.18 / σ(F): 1.39 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 2200 4.9 %
Rwork0.1653 --
obs0.1671 45121 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.79 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 26 391 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063549
X-RAY DIFFRACTIONf_angle_d0.8554799
X-RAY DIFFRACTIONf_dihedral_angle_d14.592223
X-RAY DIFFRACTIONf_chiral_restr0.056533
X-RAY DIFFRACTIONf_plane_restr0.004630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68590.27621470.20872652X-RAY DIFFRACTION97
1.6859-1.72510.23121240.20222646X-RAY DIFFRACTION97
1.7251-1.76820.25181250.18712655X-RAY DIFFRACTION98
1.7682-1.81590.24761390.17852649X-RAY DIFFRACTION98
1.8159-1.86930.23211160.1822684X-RAY DIFFRACTION98
1.8693-1.92960.18971600.17292629X-RAY DIFFRACTION98
1.9296-1.99850.20721300.17462675X-RAY DIFFRACTION98
1.9985-2.07850.20681230.16492699X-RAY DIFFRACTION98
2.0785-2.17290.21991400.16442691X-RAY DIFFRACTION99
2.1729-2.28730.19091570.17062658X-RAY DIFFRACTION99
2.2873-2.43040.19721430.16612720X-RAY DIFFRACTION99
2.4304-2.61760.22881390.17352683X-RAY DIFFRACTION99
2.6176-2.88030.24791340.17052702X-RAY DIFFRACTION99
2.8803-3.29530.17191410.16642735X-RAY DIFFRACTION99
3.2953-4.14520.16451400.14252739X-RAY DIFFRACTION99
4.1452-19.46590.18511420.15382704X-RAY DIFFRACTION97

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