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- PDB-2yoi: Crystal Structure of Ancestral Thioredoxin Relative to Last Eukar... -

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Basic information

Entry
Database: PDB / ID: 2yoi
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Eukaryotes Common Ancestor (LECA) from the Precambrian Period
ComponentsLECA THIOREDOXIN
KeywordsOXIDOREDUCTASE / ANCESTRAL RECONSTRUCTED
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGavira, J.A. / Ingles-Prieto, A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: Structure / Year: 2013
Title: Conservation of protein structure over four billion years.
Authors: Ingles-Prieto, A. / Ibarra-Molero, B. / Delgado-Delgado, A. / Perez-Jimenez, R. / Fernandez, J.M. / Gaucher, E.A. / Sanchez-Ruiz, J.M. / Gavira, J.A.
History
DepositionOct 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Atomic model
Revision 1.2Sep 25, 2013Group: Database references
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / citation / exptl_crystal_grow
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 / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method
Revision 2.1Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: LECA THIOREDOXIN
B: LECA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3089
Polymers24,0962
Non-polymers2127
Water7,476415
1
A: LECA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2377
Polymers12,0481
Non-polymers1896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LECA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0712
Polymers12,0481
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.366, 47.772, 73.836
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2075-

HOH

21B-2114-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LECA THIOREDOXIN


Mass: 12048.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: ANCESTRAL, RECONSTRUCTED PHYLOGENETICALLY / Plasmid: PET30A PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: thioredoxin-disulfide reductase

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Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.21 Å3/Da / Density % sol: 44.35 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: VAPOUR DIFFUSION, SITTING DROP; 1:1 RATIO MAGNESIUM ACETATE TETRAHYDRATE, 20% PEG 3350 T 293 K, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.973
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.3→36.6 Å / Num. obs: 46574 / % possible obs: 94.4 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 11.12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 7.9 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 1.3→25.583 Å / SU ML: 0.1 / σ(F): 0.79 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 2361 5.1 %
Rwork0.156 --
obs0.1575 46540 94.05 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.505 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.9787 Å20 Å2-0.3658 Å2
2---0.2228 Å20 Å2
3----0.7558 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 10 415 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112006
X-RAY DIFFRACTIONf_angle_d1.2872750
X-RAY DIFFRACTIONf_dihedral_angle_d14.262825
X-RAY DIFFRACTIONf_chiral_restr0.079305
X-RAY DIFFRACTIONf_plane_restr0.007361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32650.22721080.18922327X-RAY DIFFRACTION86
1.3265-1.35540.21981200.18572565X-RAY DIFFRACTION92
1.3554-1.38690.19931330.18452532X-RAY DIFFRACTION92
1.3869-1.42160.21161450.17362510X-RAY DIFFRACTION92
1.4216-1.460.18181360.16592571X-RAY DIFFRACTION93
1.46-1.5030.19431280.15862560X-RAY DIFFRACTION93
1.503-1.55150.16311390.15362536X-RAY DIFFRACTION93
1.5515-1.60690.17721280.1512545X-RAY DIFFRACTION93
1.6069-1.67130.19931320.1522604X-RAY DIFFRACTION93
1.6713-1.74730.18371590.15992564X-RAY DIFFRACTION94
1.7473-1.83940.20351270.16212612X-RAY DIFFRACTION94
1.8394-1.95460.16431240.15652642X-RAY DIFFRACTION95
1.9546-2.10550.20041420.14862693X-RAY DIFFRACTION97
2.1055-2.31720.15641690.13912673X-RAY DIFFRACTION97
2.3172-2.65220.16661630.1452712X-RAY DIFFRACTION98
2.6522-3.34030.17371660.14482717X-RAY DIFFRACTION98
3.3403-25.58820.20571420.16672816X-RAY DIFFRACTION98
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)
11.59410.3226-0.83224.0723-3.08934.94160.2581-0.132-0.15080.3528-0.1834-0.12890.2625-0.01750.31130.1926-0.046-0.05760.0360.03860.0396-5.7293-0.660233.5299
20.98370.50320.4462.7085-1.02980.84830.1177-0.219-0.05390.4957-0.08790.20230.2542-0.4085-0.11260.2832-0.14730.04250.2117-0.01450.0819-16.5245-2.620437.4104
33.15-2.0971-1.87876.26232.94923.82870.0081-0.04190.03830.056-0.0377-0.0638-0.0201-0.17010.03580.0275-0.017-0.00880.06020.00030.03-10.5653-0.656525.4927
42.6958-0.0898-0.57956.11463.22413.7053-0.02280.12140.0915-0.0810.0864-0.3382-0.34110.1825-0.0960.0786-0.0481-0.01330.0750.01830.0688-2.69185.231221.2279
53.37650.2242-0.44211.89841.05892.31850.0349-0.05080.49110.1814-0.0786-0.056-0.406-0.06180.00450.1655-0.0084-0.01270.0571-0.00330.105-8.81798.281529.8461
62.92681.343-0.18072.5384-1.94492.26610.0398-0.06640.04660.1281-0.09120.08470.2577-0.27380.01910.1072-0.06380.02610.1027-0.04730.0919-15.0706-8.739425.5352
74.1457-0.1145-2.082.9192-0.05343.0947-0.0215-0.19670.09340.0669-0.0290.3715-0.238-0.48450.04890.05990.0181-0.01970.1748-0.0230.1215-18.88594.582624.3171
86.3015-1.106-2.24074.093-1.06114.4536-0.1134-0.02240.35310.08430.0319-0.025-0.4981-0.09860.01580.1749-0.0037-0.08470.05620.0230.1015-13.3812.088719.1752
96.2974-1.84543.11110.98380.22975.66930.3106-0.2298-0.5040.4596-0.0863-0.15450.4057-0.1514-0.18750.1617-0.0114-0.05220.05360.01870.1619-11.2065-28.913414.7954
100.00770.1490.01072.9568-0.00095.6398-0.0546-0.0364-0.38370.11220.1667-0.44680.38750.7585-0.09510.12050.065-0.03420.1978-0.0730.2733-2.6029-27.53048.5641
111.9276-0.25930.05833.27791.55953.00510.0962-0.0669-0.01510.3357-0.1741-0.08530.2051-0.06940.06090.0627-0.03810.00640.064-0.01070.0747-13.886-21.536711.4547
123.50690.1207-0.64063.89162.77945.13990.10690.0484-0.11540.0934-0.12310.17990.0641-0.17610.03410.039-0.05180.04110.0816-0.0150.0898-23.7937-23.316712.6611
134.13232.57043.51335.40784.30437.48250.05780.0814-0.17440.029-0.0153-0.02340.0637-0.1057-0.05650.04490.0020.00450.0505-0.00650.0659-15.9549-27.75086.5863
142.59750.57791.79088.7957-3.42822.92450.2012-0.0721-0.12740.64890.0375-0.24220.37650.2328-0.0630.21020.019-0.06990.0667-0.04150.1088-5.1996-18.465417.9243
152.58180.8181-0.13052.2441.05813.810.02680.0832-0.05660.0397-0.0309-0.11470.15440.10320.00170.02020.0010.01260.05580.0170.0928-10.8458-16.89276.9173
163.8775-0.0233-0.80813.120.72883.9709-0.03040.15460.066-0.18140.0080.2664-0.0048-0.25930.03610.046-0.0074-0.00620.09390.02930.1062-19.3116-17.57371.1791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:7)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 8:17)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 18:31)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 32:47)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 48:58)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 59:75)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 76:93)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 94:106)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 1:7)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 8:17)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 18:31)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 32:47)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 48:58)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 59:68)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 69:83)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 84:106)

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