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- PDB-5g31: Crystallographic structure of mutant C73S of thioredoxin from Lit... -

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Basic information

Entry
Database: PDB / ID: 5g31
TitleCrystallographic structure of mutant C73S 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
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
A: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0082
Polymers11,9431
Non-polymers651
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.444, 63.444, 56.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

21A-2046-

HOH

31A-2054-

HOH

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Components

#1: Protein THIOREDOXIN


Mass: 11942.645 Da / Num. of mol.: 1 / 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: PET22B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1PWB9, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.36 Å3/Da / Density % sol: 47.89 % / Description: NONE
Crystal growpH: 8
Details: 20 % (W/V) POLYETHYLENE GLYCOL 3,000. 100 MM IMIDAZOLE PH 8.0. 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: 2→44.86 Å / Num. obs: 8227 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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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: 2→44.862 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 820 10 %
Rwork0.2081 --
obs0.2113 8198 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.66 Å2
Refinement stepCycle: LAST / Resolution: 2→44.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 1 54 888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008892
X-RAY DIFFRACTIONf_angle_d0.9081210
X-RAY DIFFRACTIONf_dihedral_angle_d13.034560
X-RAY DIFFRACTIONf_chiral_restr0.054133
X-RAY DIFFRACTIONf_plane_restr0.005162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.27641330.21781199X-RAY DIFFRACTION100
2.1253-2.28940.26311330.21761194X-RAY DIFFRACTION100
2.2894-2.51980.28681340.2161205X-RAY DIFFRACTION100
2.5198-2.88430.27171350.221221X-RAY DIFFRACTION100
2.8843-3.63370.26271380.20851238X-RAY DIFFRACTION100
3.6337-44.8730.19671470.19841321X-RAY DIFFRACTION100

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