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- PDB-4x43: Structure of proline-free E. coli Thioredoxin -

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Basic information

Entry
Database: PDB / ID: 4x43
TitleStructure of proline-free E. coli Thioredoxin
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / Protein folding / THIOREDOXIN FOLD / PROTEIN DISULFIDE OXIDOREDUCTASE ACTIVITY / REDOX PROTEIN
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
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsScharer, M.A. / Glockshuber, R.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
ETH Zurich Switzerland
Swiss National Science Foundation Switzerland
CitationJournal: Sci Rep / Year: 2015
Title: Acceleration of protein folding by four orders of magnitude through a single amino acid substitution.
Authors: Roderer, D.J. / Scharer, M.A. / Rubini, M. / Glockshuber, R.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-1
B: Thioredoxin-1
C: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)34,6723
Polymers34,6723
Non-polymers00
Water5,116284
1
A: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,5571
Polymers11,5571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,5571
Polymers11,5571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,5571
Polymers11,5571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.670, 48.570, 89.940
Angle α, β, γ (deg.)90.000, 101.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin-1 / Trx-1 / Trx0P


Mass: 11557.201 Da / Num. of mol.: 3 / Mutation: P34A, P40A, P64A, P68A, P76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trxA, fipA, tsnC, b3781, JW5856 / Plasmid: pTRX0P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2013
RadiationMonochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.65→44.1 Å / Num. obs: 35498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 20.83 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.145 / Χ2: 0.93 / Net I/σ(I): 14.04 / Num. measured all: 437002
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.690.42.0311.1430727258825772.1299.6
1.69-1.740.4941.7361.3630993257325721.811100
1.74-1.790.6351.4161.7330010244324481.476100
1.79-1.840.7481.1492.1829445240924021.19999.7
1.84-1.910.8220.9152.8228445231223160.954100
1.91-1.970.8840.6773.7326038226822610.70899.7
1.97-2.050.9320.5324.9326753221622190.556100
2.05-2.130.9540.4436.327447209420940.461100
2.13-2.220.9760.338.2826040200420000.34499.8
2.22-2.330.9810.25810.5424772192019210.268100
2.33-2.460.990.21212.4623520183518380.22100
2.46-2.610.9930.1715.1721393173217280.17899.8
2.61-2.790.9930.13817.7518609162416250.144100
2.79-3.010.9970.10124.2718879155415520.10599.9
3.01-3.30.9990.07333.7618277139813980.076100
3.3-3.690.9990.05643.6316193126812680.058100
3.69-4.260.9990.04252.9114382116011610.044100
4.26-5.220.9990.03656.58105839409370.03799.7
5.22-7.380.9990.0454.3692257567550.04299.9
7.3810.02677.5752714304270.02799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.63 Å44.14 Å
Translation2.63 Å44.14 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hu7

4hu7


Resolution: 1.65→44.1 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 924 2.6 %
Rwork0.1758 34574 -
obs0.1769 35498 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.92 Å2 / Biso mean: 28.9816 Å2 / Biso min: 12.29 Å2
Refinement stepCycle: final / Resolution: 1.65→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 0 284 2700
Biso mean---34.26 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082505
X-RAY DIFFRACTIONf_angle_d1.0163392
X-RAY DIFFRACTIONf_chiral_restr0.045400
X-RAY DIFFRACTIONf_plane_restr0.004432
X-RAY DIFFRACTIONf_dihedral_angle_d12.377889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6501-1.73710.3461080.288349245032
1.7371-1.84590.2861180.257948895007
1.8459-1.98850.24731440.216848995043
1.9885-2.18860.22221320.194649275059
2.1886-2.50520.23741410.186149395080
2.5052-3.15620.24781440.17749535097
3.1562-44.15850.16711370.135250435180
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)
13.40090.9619-2.31185.5041-0.18736.9830.1599-0.2695-0.09450.3757-0.5040.61850.4368-1.00920.18020.2138-0.11160.03650.3856-0.05830.2457-22.3966-2.6857-21.9685
23.80470.53210.15513.8429-1.40496.51720.1433-0.26130.01560.1994-0.08410.01780.1575-0.1585-0.04180.1485-0.0230.00010.1286-0.01790.1138-12.3714-0.0658-20.8245
37.31013.3964-6.13946.5965-3.30746.83670.0263-0.1182-0.5027-0.0382-0.1618-0.37510.88440.12730.06960.3274-0.0307-0.06140.2077-0.03840.1957-7.0743-8.3314-24.2994
44.78562.61374.06079.49774.98146.421-0.2862-0.06790.3275-0.0066-0.09320.306-0.6135-0.14250.390.24850.0113-0.00190.1606-0.01630.2062-14.80647.7336-26.664
53.83011.142-0.87225.0263-4.28967.5270.02480.0964-0.0696-0.2378-0.0222-0.13940.8520.13120.01840.34290.0241-0.02370.25170.01560.1654-3.2785-6.2293-14.2199
64.48731.299-1.55743.14581.32395.6638-0.048-0.0849-0.12410.2124-0.0011-0.19910.29740.12340.06420.13420.0136-0.01660.08940.01520.25691.9527-20.6076-38.552
75.67080.78052.72434.38572.42554.18090.1434-0.15480.03650.1369-0.146-0.07970.091-0.205-0.01080.0687-0.01580.02070.0960.01790.16380.9472-10.1053-39.3123
85.4835-1.85111.49633.492-0.88753.4326-0.11110.40090.1163-0.2794-0.0353-0.17360.04640.15970.13720.1476-0.03240.03570.1168-0.04140.27076.0083-9.2428-48.4455
95.2115-0.8320.94188.71384.0393.97570.0045-0.21570.15680.0639-0.14490.8627-0.2508-0.42680.13490.16140.01830.05810.16240.00970.2671-9.4361-11.3388-38.2209
102.9024-0.0260.73523.9254-1.86666.9687-0.0730.04960.2571-0.19530.1558-0.0780.06020.0284-0.07310.1237-0.02270.00270.0924-0.00140.213810.4815-2.7867-42.162
112.46040.51352.27258.46030.89399.1373-0.26750.3395-0.0317-0.95290.2152-0.5848-0.36730.52420.17220.3467-0.05590.04220.3409-0.00030.25430.542218.3584-18.1936
127.5374-0.0551.32342.8721-1.23262.7530.08250.1465-0.1118-0.1404-0.10480.11570.1222-0.11240.02990.2477-0.0242-0.03360.2203-0.0560.1413-3.479414.6399-9.4436
132.3836-0.58880.53751.31170.16181.9948-0.0626-0.27540.20830.05870.0271-0.0579-0.1974-0.00940.06560.2664-0.0215-0.01310.2332-0.03370.1857-0.001922.0594-2.9055
146.4987-3.62180.90967.15810.48936.7031-0.11940.2469-0.01870.4214-0.15270.2159-0.0621-0.76590.30690.2346-0.0019-0.03660.2793-0.0740.1753-12.360314.1112-14.5362
157.43892.3014.91736.5929-0.64094.72480.2988-0.2828-0.34460.3571-0.0254-0.42250.45530.008-0.25560.3074-0.0344-0.04540.21540.00030.13692.305413.06291.4653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 21 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)A22
3X-RAY DIFFRACTION2chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)A54
4X-RAY DIFFRACTION2chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)A75
5X-RAY DIFFRACTION3chain 'A' and (resid 31 through 53 )A0
6X-RAY DIFFRACTION4chain 'A' and (resid 61 through 74 )A0
7X-RAY DIFFRACTION5chain 'A' and (resid 92 through 108 )A0
8X-RAY DIFFRACTION6chain 'B' and (resid 1 through 21 )B0
9X-RAY DIFFRACTION7chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)B22
10X-RAY DIFFRACTION7chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)B54
11X-RAY DIFFRACTION7chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)B75
12X-RAY DIFFRACTION8chain 'B' and (resid 31 through 53 )B0
13X-RAY DIFFRACTION9chain 'B' and (resid 61 through 74 )B0
14X-RAY DIFFRACTION10chain 'B' and (resid 92 through 108 )B0
15X-RAY DIFFRACTION11chain 'C' and (resid 2 through 21 )C0
16X-RAY DIFFRACTION12chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)C22
17X-RAY DIFFRACTION12chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)C54
18X-RAY DIFFRACTION12chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)C75
19X-RAY DIFFRACTION13chain 'C' and (resid 31 through 53 )C0
20X-RAY DIFFRACTION14chain 'C' and (resid 61 through 74 )C0
21X-RAY DIFFRACTION15chain 'C' and (resid 92 through 108 )C0

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