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- PDB-1zzy: Crystal Structure of Thioredoxin Mutant L7V -

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Basic information

Entry
Database: PDB / ID: 1zzy
TitleCrystal Structure of Thioredoxin Mutant L7V
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / Alpha/Beta
Function / homology
Function and homology information


positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / oxidoreductase activity / cytoplasm / cytosol
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
Thioredoxin 1 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: To be Published
Title: Crystal Structure of Thioredoxin Mutant L7V
Authors: Gavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
History
DepositionJun 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Experimental preparation
Category: database_2 / exptl_crystal_grow / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)23,3472
Polymers23,3472
Non-polymers00
Water63135
1
A: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.658, 36.597, 42.836
Angle α, β, γ (deg.)78.43, 67.38, 88.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thioredoxin 1 / TRX1 / TRX


Mass: 11673.360 Da / Num. of mol.: 2 / Mutation: L7V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, fipA, tsnC / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / References: UniProt: P00274, UniProt: P0AA25*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 295 K / Method: counter-diffusion / pH: 3.8
Details: 10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 7, 2005 / Details: Montel Optics
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40.26 Å / Num. all: 5671 / Num. obs: 5671 / % possible obs: 88.7 % / Redundancy: 1.46 % / Biso Wilson estimate: 12.8 Å2 / Limit h max: 13 / Limit h min: -12 / Limit k max: 14 / Limit k min: -12 / Limit l max: 17 / Limit l min: 0 / Observed criterion F max: 1312437.97 / Observed criterion F min: 3.46 / Rsym value: 0.1236 / Net I/σ(I): 6.57
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.38 % / Mean I/σ(I) obs: 2.82 / Num. unique all: 605 / Rsym value: 0.374 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PROTEUM2data collection
SAINTdata reduction
SADABSdata reduction
XPREPdata reduction
CNSrefinement
PROTEUM PLUS2data reduction
SAINTdata scaling
SADABSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A:2trx.pdb

2trx


Resolution: 2.5→38.69 Å / Rfactor Rfree error: 0.016 / Occupancy max: 1 / Occupancy min: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: XTALVIEW and MOLBROBITY were also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 283 5.1 %random
Rwork0.223 ---
all-6393 --
obs-5499 86 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.8937 Å2 / ksol: 0.324627 e/Å3
Displacement parametersBiso max: 72.55 Å2 / Biso mean: 23.29 Å2 / Biso min: 1.01 Å2
Baniso -1Baniso -2Baniso -3
1-11.2 Å2-2.5 Å2-2.15 Å2
2---4.83 Å21.02 Å2
3----6.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.38 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 35 1649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.442335.30.315930.07779962678.3
2.61-2.750.453365.60.3116100.07679864681
2.75-2.920.254253.60.2416630.05179368886.8
2.92-3.150.291456.20.2276790.04380072490.5
3.15-3.470.266415.60.2326890.04279673091.7
3.47-3.970.248415.60.1926910.03981173290.3
3.97-50.21365.10.1636650.03579470188.2
5-38.690.2112640.2326260.04180565281
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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