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- PDB-2h6y: Crystal Structure of Thioredoxin Mutant E48D in Hexagonal (p61) S... -

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Basic information

Entry
Database: PDB / ID: 2h6y
TitleCrystal Structure of Thioredoxin Mutant E48D 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 / molecular replacement / Resolution: 2.4 Å
AuthorsGavira, J.A. / Godoy-Ruiz, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
Citation
Journal: To be Published
Title: Crystal Structure of Thioredoxin Mutant E48D 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, R. / Sanchez-Ruiz, R.
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: Advisory / Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / exptl_crystal_grow ...database_2 / exptl_crystal_grow / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 20, 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
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5834
Polymers23,3472
Non-polymers2362
Water1,58588
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9103
Polymers11,6731
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.608, 101.608, 38.658
Angle α, β, γ (deg.)90.00, 90.00, 120
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Thioredoxin


Mass: 11673.361 Da / Num. of mol.: 2 / Mutation: E48D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / 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.: 88 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 3.5
Details: 60% (v/v) MPD, AcNa 15 mM pH 3.5, 1 mM Ac2Cu, Counter-diffusion, 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: Dec 20, 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: 2.4→50.8 Å / Num. all: 9093 / Num. obs: 9093 / % possible obs: 99.5 % / Redundancy: 10.25 % / Biso Wilson estimate: 35.742 Å2 / Rsym value: 0.048 / Net I/σ(I): 18.96
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.45 / Num. unique all: 492 / Rsym value: 0.3529 / % possible all: 93.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
PROTEUM PLUS2data reduction
SADABSdata scaling
XPREPdata reduction
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX_A

Resolution: 2.4→50.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.174 / SU B: 15.511 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 408 4.763 %RANDOM
Rwork0.1864 ---
all0.188 9093 --
obs0.188 8566 93.915 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.717 Å2
Baniso -1Baniso -2Baniso -3
1--1.442 Å2-0.721 Å20 Å2
2---1.442 Å20 Å2
3---2.163 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 16 88 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221728
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9912360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26126.95769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.32151
X-RAY DIFFRACTIONr_chiral_restr0.0720.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021279
X-RAY DIFFRACTIONr_nbd_refined0.1950.2742
X-RAY DIFFRACTIONr_nbtor_refined0.30.21165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.211
X-RAY DIFFRACTIONr_mcbond_it0.3691.51118
X-RAY DIFFRACTIONr_mcangle_it0.66521759
X-RAY DIFFRACTIONr_scbond_it0.8973686
X-RAY DIFFRACTIONr_scangle_it1.4784.5595
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.4-2.4620.297240.2324970.23666278.701
2.462-2.530.29220.2055210.20864284.579
2.53-2.6030.326270.2265290.23163787.284
2.603-2.6830.21230.1995250.19959592.101
2.683-2.770.338260.215320.21760692.079
2.77-2.8670.334250.225290.22657895.848
2.867-2.9750.234250.2085100.2156195.365
2.975-3.0960.27290.1964900.20153497.191
3.096-3.2330.204230.1764830.17851698.062
3.233-3.390.236290.1794580.18249698.185
3.39-3.5730.238260.1714290.17546697.639
3.573-3.7890.174160.1694240.16944798.434
3.789-4.0490.153190.1574000.15642399.054
4.049-4.3710.215220.1463670.14939498.731
4.371-4.7840.179140.1523430.15336099.167
4.784-5.3430.245120.1723210.17533699.107
5.343-6.1580.176170.1962720.195289100
6.158-7.5150.215100.2292490.229259100
7.515-10.5130.172120.1671830.167195100
10.513-50.80.1970.299960.2912582.4
Refinement TLS params.Method: refined / Origin x: -4.134 Å / Origin y: 37.109 Å / Origin z: 18.29 Å
111213212223313233
T-0.0641 Å2-0.0107 Å2-0.0035 Å2--0.103 Å20.0055 Å2---0.0982 Å2
L2.8275 °2-1.1784 °20.2307 °2-1.9341 °2-0.1105 °2--0.4746 °2
S-0.0249 Å °-0.0145 Å °0.1356 Å °0.0069 Å °0.0253 Å °0.0126 Å °-0.1042 Å °-0.067 Å °-0.0003 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 2 - 108 / Label seq-ID: 2 - 108

IDAuth asym-IDLabel asym-ID
1AA
2BB

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