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- PDB-2h74: Crystal Structure of Thioredoxin Mutant D2E in Hexagonal (p61) Sp... -

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Basic information

Entry
Database: PDB / ID: 2h74
TitleCrystal Structure of Thioredoxin Mutant D2E 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: 2.4 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 D2E 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: 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 / pdbx_initial_refinement_model

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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
Water1,08160
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
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7011
Polymers11,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.497, 103.497, 41.780
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: 11701.413 Da / Num. of mol.: 2 / Mutation: D2E
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.: 60 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 3.5
Details: 60% (v/v) MPD, AcNa 15 mM pH3.5, Ac2Cu 1 mM, 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: 2.4→44.82 Å / Num. all: 10198 / Num. obs: 10198 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 49.79 Å2 / Rsym value: 0.0242 / Net I/σ(I): 32.58
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.89 % / Mean I/σ(I) obs: 4.36 / Num. unique all: 605 / Rsym value: 0.2876 / % possible all: 97.9

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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: 2.4→44.82 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.186 / SU B: 18.311 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1014 9.978 %Random
Rwork0.2007 ---
all0.206 10198 --
obs0.206 10162 99.471 %-
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: 20.845 Å2
Baniso -1Baniso -2Baniso -3
1--2.785 Å2-1.392 Å20 Å2
2---2.785 Å20 Å2
3---4.177 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 16 60 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221739
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9922365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01327.10169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.366151
X-RAY DIFFRACTIONr_chiral_restr0.0940.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021277
X-RAY DIFFRACTIONr_nbd_refined0.220.2688
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.27
X-RAY DIFFRACTIONr_mcbond_it1.2721150
X-RAY DIFFRACTIONr_mcangle_it1.9331775
X-RAY DIFFRACTIONr_scbond_it1.2262684
X-RAY DIFFRACTIONr_scangle_it1.7893588
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 (%)
2.4-2.4620.376820.2386630.25476397.641
2.462-2.5290.392720.2426420.258714100
2.529-2.6030.383760.2466450.25972399.723
2.603-2.6820.31690.225780.2365299.233
2.682-2.770.305770.256130.256690100
2.77-2.8670.363670.2255690.23963799.843
2.867-2.9750.347600.245620.249622100
2.975-3.0950.264520.2055460.21598100
3.095-3.2320.224620.195230.19358699.829
3.232-3.3890.231620.24840.204546100
3.389-3.5710.215500.1884770.19152899.811
3.571-3.7870.251550.1744440.18350299.402
3.787-4.0460.237390.1724170.17845899.563
4.046-4.3670.178400.1574100.159450100
4.367-4.7790.237420.1483590.157401100
4.779-5.3360.249260.1813510.185377100
5.336-6.1470.254310.2342940.236325100
6.147-7.4930.252280.232540.232282100
7.493-10.4520.17170.1852070.18422599.556
10.452-44.820.17970.3381100.32713785.401
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)
117.9901-3.8842-2.990212.99110.402618.7709-0.9414-1.1508-1.79172.14830.1228-0.72740.44740.20170.81870.0585-0.0003-0.0666-0.15370.27820.26998.032318.832424.6024
24.4077-2.63620.01338.079-1.90350.55260.19140.4999-0.5814-0.7159-0.09490.51910.2196-0.423-0.0964-0.0916-0.0592-0.0785-0.0492-0.05510.02470.44520.201913.175
311.2031-1.6697-0.88181.8705-0.11931.2037-0.03870.0215-0.7362-0.1076-0.0417-0.2290.06710.00150.0803-0.18690.00710.0032-0.17450.0131-0.02375.831926.939618.2792
413.78961.0901-5.16482.8677-2.766411.22450.345-1.1009-0.43220.7519-0.3091-1.2819-0.62330.4533-0.0359-0.0997-0.0364-0.1353-0.10810.07510.125314.167229.665226.3249
57.9071-1.2036-5.34676.39034.63265.96480.3503-0.5613-0.86220.7588-0.0636-0.19070.08230.0539-0.2868-0.0644-0.0203-0.0876-0.0930.16490.06894.201124.8828.4759
611.6756-3.6506-1.12114.0340.98680.24760.1151.049-0.3375-0.2420.00520.02960.0034-0.1392-0.1202-0.08550.0090.00850.0120.0525-0.1346.871227.95749.2795
711.2444-0.13090.22933.91511.15760.34870.17790.55480.0523-0.1979-0.1476-0.2239-0.2472-0.1131-0.0303-0.1190.0077-0.0521-0.15030.0348-0.08524.166533.474817.4334
85.8952.63080.77366.1332-1.01646.4869-0.23170.2837-0.1-0.03380.05870.1-0.1661-0.23680.173-0.18690.014-0.0198-0.17870.0268-0.0925-3.084133.500419.8481
96.94411.434-2.23424.9404-1.551215.79680.0184-0.7260.34670.4859-0.1344-0.7283-0.26020.24440.116-0.0428-0.0325-0.1562-0.14060.01260.01338.129337.469428.3723
1026.4897-16.20593.153610.95631.884714.33780.1215-1.46170.12151.1174-0.0551-0.1335-0.6335-0.7458-0.06640.0239-0.0344-0.002-0.08630.0533-0.053-2.244835.22330.1165
1125.338223.2067-14.117421.2544-12.92977.8656-0.69950.56822.9473-2.9880.3056-1.4038-1.2267-2.53720.39390.10850.2978-0.07810.23010.65220.3819-11.826751.42596.0737
1213.81425.99010.03163.02931.76417.0948-0.3054-0.28262.29430.40290.3468-0.5844-0.7466-0.4413-0.04140.09660.0938-0.0922-0.06990.12940.5989-11.845157.371618.4046
131.4267-0.57050.71195.1909-2.35951.39570.0323-0.27110.15840.10820.31550.6763-0.2095-0.2124-0.34780.03940.0559-0.06350.02440.17210.1141-16.756850.554417.4025
147.12982.51145.044614.022910.2569.04140.0570.7890.755-0.62760.0804-0.8467-0.5753-0.1173-0.1374-0.11380.02240.0184-0.01910.21910.0131-0.509642.307412.1088
1542.2904-12.73394.57986.38-0.85580.60350.85631.69540.0386-1.4166-0.6980.62040.151-0.2976-0.15840.09210.145-0.19330.38890.1746-0.0856-15.618641.77245.1223
1612.0296-1.76916.24815.16752.62625.80620.0690.31251.3772-0.4629-0.0793-0.1876-0.3997-0.37220.01030.00920.03840.0073-0.02940.26140.1735-9.715649.592613.8081
1724.2103-0.1556-7.63259.89754.99424.8772-0.719-0.75761.08710.53370.341-0.0986-0.43580.3620.37810.11620.1623-0.09520.01150.011-0.057-6.857348.712825.9445
1812.841-2.7489-1.66337.8341.46930.5608-0.5952-0.06990.59580.71840.37380.5886-0.3342-0.1210.22140.03950.0577-0.0446-0.09140.1333-0.0084-15.913245.080921.463
199.1346-2.76252.611319.73122.28996.76370.28390.4617-0.5713-0.51420.14190.04620.17560.2693-0.4258-0.1081-0.0243-0.1327-0.15810.0779-0.0752-12.014235.649414.9314
2020.49813.344-2.01166.3507-1.97559.2180.580.0293-0.7544-0.6092-0.08861.0299-0.306-0.6157-0.4914-0.04670.0198-0.16030.00390.09580.0368-20.911736.15714.3292
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 71 - 7
22AA8 - 168 - 16
33AA17 - 3317 - 33
44AA34 - 4534 - 45
55AA46 - 5846 - 58
66AA59 - 7259 - 72
77AA73 - 8273 - 82
88AA83 - 9083 - 90
99AA91 - 10291 - 102
1010AA103 - 108103 - 108
1111BB1 - 61 - 6
1212BB7 - 167 - 16
1313BB17 - 2717 - 27
1414BB28 - 3828 - 38
1515BB39 - 5039 - 50
1616BB51 - 6351 - 63
1717BB64 - 7364 - 73
1818BB74 - 8974 - 89
1919BB90 - 9790 - 97
2020BB98 - 10898 - 108

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