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- PDB-2fd3: Crystal Structure of Thioredoxin Mutant P34H -

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Basic information

Entry
Database: PDB / ID: 2fd3
TitleCrystal Structure of Thioredoxin Mutant P34H
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / Alpha Beta
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: To be Published
Title: Crystal Structure of Thioredoxin Mutant P34H
Authors: Gavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Oct 16, 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)23,4572
Polymers23,4572
Non-polymers00
Water1,63991
1
A: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7281
Polymers11,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7281
Polymers11,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.138, 90.041, 36.326
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 1 - 108 / Label seq-ID: 1 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Thioredoxin 1 / TRX1 / TRX


Mass: 11728.420 Da / Num. of mol.: 2 / Mutation: P34H
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: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 8
Details: 60% (v/v) MPD, Hepes 15 mM, 1 mM Ac2Cu, pH 8.0, Counter-diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Nov 28, 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: 2.45→18.674 Å / Num. all: 4223 / Num. obs: 4223 / % possible obs: 61.9 % / Redundancy: 1.19 % / Biso Wilson estimate: 31.13 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.88
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 0.61 % / Mean I/σ(I) obs: 3.06 / Num. unique all: 189 / Rsym value: 0.3084 / % possible all: 47.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PROTEUM PLUS2data reduction
SAINTdata scaling
SADABSdata scaling
XPREPdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2TRX_A

Resolution: 2.45→16.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.849 / SU B: 11.223 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MolProbity, Xtalview were also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.30495 193 4.6 %RANDOM
Rwork0.17983 ---
obs0.18527 4013 62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.073 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.4 Å2
2--0.56 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.45→16.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 0 91 1776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9762331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80326.75774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72215309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.315152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21134
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.86721118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39931736
X-RAY DIFFRACTIONr_scbond_it0.7422688
X-RAY DIFFRACTIONr_scangle_it1.1323595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 802 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.45
loose thermal1.3110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.5120.575110.22822048.23
2.512-2.5790.349110.22549.79
2.579-2.6520.255140.19857.33
2.652-2.7320.293140.22866.67
2.732-2.8190.313150.20964.81
2.819-2.9150.421180.24771.679

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