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- PDB-2h6x: Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Spa... -

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Basic information

Entry
Database: PDB / ID: 2h6x
TitleCrystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group
ComponentsThioredoxin
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
Thioredoxin 1 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGavira, J.A. / Godoy-Ruiz, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
Citation
Journal: To be Published
Title: Crystal Structure of Thioredoxin Wild Type in Hexagonal (p61) Space Group
Authors: Godoy-Ruiz, R. / Gavira, J.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations
Authors: Godoy-Ruiz, R. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / 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 / _exptl_crystal_grow.method / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6114
Polymers23,3752
Non-polymers2362
Water1,49583
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9243
Polymers11,6871
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6871
Polymers11,6871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.727, 102.727, 42.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Thioredoxin


Mass: 11687.388 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: peT30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2M889, UniProt: P0AA25*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 3.5
Details: 60% (v/v) MPD, Ac2Cu 1mM, AcNa 15mM, HEPES 15 mM pH 6.9, pH 3.5, Counterdiffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 28, 2006 / 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: 2.6→51.36 Å / Num. all: 8147 / Num. obs: 8147 / % possible obs: 99.8 % / Redundancy: 7.28 % / Biso Wilson estimate: 51.288 Å2 / Rsym value: 0.0787 / Net I/σ(I): 9.08
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 7.28 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 464 / Rsym value: 0.3161 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
PROTEUM PLUS2data reduction
SAINTdata scaling
SADABSdata scaling
XPREPdata reduction
AMoREphasing
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2TRX

2trx


Resolution: 2.6→44.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.219 / SU B: 15.605 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.95 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 370 4.6 %RANDOM
Rwork0.219 ---
all0.222 8147 --
obs0.222 8077 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.24 Å20 Å2
2---0.48 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 16 83 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221711
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9922328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22426.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.798152
X-RAY DIFFRACTIONr_chiral_restr0.0830.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021248
X-RAY DIFFRACTIONr_nbd_refined0.2230.2836
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.23
X-RAY DIFFRACTIONr_mcbond_it1.19321110
X-RAY DIFFRACTIONr_mcangle_it1.95431743
X-RAY DIFFRACTIONr_scbond_it1.1422656
X-RAY DIFFRACTIONr_scangle_it1.6363583
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6670.442270.285581608100
2.667-2.740.413190.355057099.825
2.74-2.8190.355300.31253656799.824
2.819-2.9060.429250.282518543100
2.906-3.0010.383250.28850653399.625
3.001-3.1050.286270.22948351599.029
3.105-3.2220.461200.24846448899.18
3.222-3.3530.271250.23545648599.175
3.353-3.5010.424220.22943145799.125
3.501-3.6710.382150.23142444498.874
3.671-3.8680.212210.20438440999.022
3.868-4.1010.232130.19838140298.01
4.101-4.3810.265150.18634936699.454
4.381-4.7280.31180.17634036199.169
4.728-5.1740.131140.17307321100
5.174-5.7750.246170.203278295100
5.775-6.6490.212110.211252263100
6.649-8.0990.276140.201212226100
8.099-11.2680.158100.138170180100
11.268-44.4990.2420.3378511178.378

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