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- PDB-2h73: Crystal Structure of Thioredoxin Mutant D43E in Hexagonal (p61) S... -

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Basic information

Entry
Database: PDB / ID: 2h73
TitleCrystal Structure of Thioredoxin Mutant D43E 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 / cytosol / cytoplasm
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: 2.45 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 D43E 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, 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: Advisory / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
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 1.6Aug 30, 2023Group: 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

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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)23,6394
Polymers23,4032
Non-polymers2362
Water1,42379
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9383
Polymers11,7011
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7011
Polymers11,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.991, 102.991, 42.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

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: 3 / Auth seq-ID: 1 - 108 / Label seq-ID: 1 - 108

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

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Components

#1: Protein Thioredoxin /


Mass: 11701.413 Da / Num. of mol.: 2 / Mutation: D43E
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.67 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 7
Details: 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, 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 / 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→44.6 Å / Num. all: 9672 / Num. obs: 9672 / % possible obs: 99.9 % / Redundancy: 9.43 % / Biso Wilson estimate: 49.495 Å2 / Rsym value: 0.0319 / Net I/σ(I): 22.19
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 8.26 % / Mean I/σ(I) obs: 3.93 / Num. unique all: 574 / Rsym value: 0.2322 / % possible all: 100

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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: pdb entry 2TRX

2trx


Resolution: 2.45→44.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.192 / SU B: 20.876 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: Throuhgout / ESU R: 0.497 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 462 4.818 %Random
Rwork0.2088 ---
all0.212 9672 --
obs0.212 9589 99.275 %-
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: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.366 Å2-1.683 Å20 Å2
2---3.366 Å20 Å2
3---5.049 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 16 79 1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221745
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9912378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.67726.52872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75215310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.675153
X-RAY DIFFRACTIONr_chiral_restr0.1080.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021285
X-RAY DIFFRACTIONr_nbd_refined0.2430.2772
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.28
X-RAY DIFFRACTIONr_mcbond_it1.26521130
X-RAY DIFFRACTIONr_mcangle_it1.92931760
X-RAY DIFFRACTIONr_scbond_it1.4152708
X-RAY DIFFRACTIONr_scangle_it1.9763611
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberRmsTypeWeight
4250.19TIGHT POSITIONAL0.05
3510.6LOOSE POSITIONAL5
4250.57TIGHT THERMAL0.5
3512.09LOOSE THERMAL10
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 (%)
2.45-2.5140.341500.2416670.248717100
2.514-2.5820.339310.276450.273676100
2.582-2.6570.269360.2616380.262674100
2.657-2.7380.379330.2446040.251637100
2.738-2.8280.321260.2516050.25563299.842
2.828-2.9270.352340.2465770.25161399.674
2.927-3.0360.301280.2655620.26760098.333
3.036-3.160.255260.2325130.23354399.263
3.16-3.30.312250.215140.21455197.822
3.3-3.460.266180.2295060.2352899.242
3.46-3.6460.26200.2054680.20849698.387
3.646-3.8650.26250.1954440.19947698.529
3.865-4.130.232240.1834270.18645499.339
4.13-4.4580.25170.1593920.16241299.272
4.458-4.8780.158150.1713590.17374100
4.878-5.4460.318170.1713350.178352100
5.446-6.2730.277120.1972980.2310100
6.273-7.6450.256100.2162590.218269100
7.645-10.6560.252110.1492020.15421499.533
10.656-44.60.57640.3161120.32113188.55
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
129.74270.985814.522919.0059-8.325634.1337-0.6891-1.5241.00041.4774-0.71331.2049-1.761-1.97441.40240.15850.00390.130.0787-0.27940.2373-7.978-18.4953.974
24.701-0.50971.49152.83250.47522.64160.33750.32980.07810.0206-0.16930.2961-0.09930.1582-0.16820.04680.04570.02520.0649-0.06970.1618-6.71-25.806-3.198
34.54731.53012.45626.9606-1.99259.58550.1215-0.7160.26730.7958-0.09110.2894-0.2724-0.2134-0.03030.0863-0.00290.11320.094-0.1370.2247-5.895-25.5168.297
44.6664-3.44620.49094.2483-0.78191.37130.36430.8532-0.5901-0.5373-0.35940.49350.0215-0.2307-0.00490.11570.0526-0.03170.1582-0.13190.1507-6.921-30.999-9.099
57.47182.1607-1.60915.1459-1.67474.66880.2446-0.2895-0.51770.4067-0.15120.16040.28310.0962-0.09350.08810.01350.08330.0084-0.04030.2555-1.71-35.1035.133
618.55632.783-7.180211.020214.1538-0.34110.8661-1.0683-0.21640.17520.6958-0.0021-0.69930.1660.20380.0640.00760.1899-0.27320.603611.698-55.534-6.933
74.3258-3.1434-0.01726.1039-0.06570.00170.32390.8473-0.7138-0.4395-0.21940.05820.29260.0919-0.10440.18290.10090.02230.2744-0.22150.30688.321-45.434-7.643
810.5505-1.9577-0.66657.949-1.34473.27110.05650.5923-1.018-0.07630.1531-0.06430.05980.1515-0.20960.18560.1236-0.05180.2296-0.27680.260711.754-47.98-6.199
920.4574-2.8582-2.02769.60850.25011.07730.0646-0.4484-1.12681.06420.1976-0.32540.36430.4343-0.26220.34870.088-0.04910.159-0.20610.243914.402-45.2771.31
1012.1982-1.9592-0.38139.48294.62225.54220.17940.8383-0.49050.1454-0.1853-0.4159-0.03230.26910.00590.24680.02660.17370.1974-0.12290.226717.486-36.257-5.469
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 61 - 6
22AA7 - 407 - 40
33AA41 - 5841 - 58
44AA59 - 8059 - 80
55AA81 - 10881 - 108
66BB1 - 161 - 16
77BB17 - 4317 - 43
88BB44 - 7144 - 71
99BB72 - 8772 - 87
1010BB88 - 10888 - 108

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