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- PDB-2yn1: Crystal Structure of Ancestral Thioredoxin Relative to Last Gamma... -

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Basic information

Entry
Database: PDB / ID: 2yn1
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Gamma- Proteobacteria Common Ancestor (LGPCA) from the Precambrian Period
ComponentsLGPCA THIOREDOXIN
KeywordsOXIDOREDUCTASE / ALPHA BETA / ELECTRON TRANSPORT / ANCESTRAL RECONSTRUCTED PROTEIN
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / TRIETHYLENE GLYCOL
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 11, 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 2.0Mar 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
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 / _atom_site.pdbx_auth_atom_name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 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: LGPCA THIOREDOXIN
B: LGPCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7494
Polymers23,4492
Non-polymers3002
Water6,449358
1
A: LGPCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8752
Polymers11,7251
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LGPCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8752
Polymers11,7251
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.090, 62.910, 42.910
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LGPCA THIOREDOXIN


Mass: 11724.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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 Å3/Da / Density % sol: 38.45 % / Description: NONE
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 3
Details: COUNTER-DIFFUSION TECHNIQUE. 30% PEG 400, 0.1 M TRIS-HCL, 0.2 M NA CITRATE, PH 8.50, 277K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.3→34.09 Å / Num. obs: 43308 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 12.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.47
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.68 / % possible all: 97.8

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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→34.089 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 2194 5.1 %
Rwork0.1676 --
obs0.1694 43303 97.2 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.3 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 20 358 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111901
X-RAY DIFFRACTIONf_angle_d1.352593
X-RAY DIFFRACTIONf_dihedral_angle_d12.716766
X-RAY DIFFRACTIONf_chiral_restr0.072290
X-RAY DIFFRACTIONf_plane_restr0.008339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32830.26891200.272589X-RAY DIFFRACTION98
1.3283-1.35920.26051430.26012556X-RAY DIFFRACTION97
1.3592-1.39320.22711410.24392586X-RAY DIFFRACTION98
1.3932-1.43080.26841220.22482604X-RAY DIFFRACTION98
1.4308-1.47290.25341460.21912564X-RAY DIFFRACTION98
1.4729-1.52050.24771440.20812541X-RAY DIFFRACTION97
1.5205-1.57480.19781410.19652553X-RAY DIFFRACTION96
1.5748-1.63790.22481320.19062495X-RAY DIFFRACTION95
1.6379-1.71240.21621580.17422576X-RAY DIFFRACTION98
1.7124-1.80270.20931490.16592575X-RAY DIFFRACTION98
1.8027-1.91560.18941280.15722542X-RAY DIFFRACTION97
1.9156-2.06350.15541390.14462543X-RAY DIFFRACTION97
2.0635-2.27110.2031290.14622618X-RAY DIFFRACTION98
2.2711-2.59970.2091260.15372581X-RAY DIFFRACTION97
2.5997-3.27490.20291370.15682580X-RAY DIFFRACTION96
3.2749-34.10070.18761390.15112606X-RAY DIFFRACTION97
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)
11.83160.8597-0.54624.8295-1.1462.5342-0.0071-0.1768-0.03610.23270.04310.0003-0.0636-0.0075-0.03510.0710.01680.00510.0801-0.00690.045112.7775-12.62423.2422
23.29490.50350.10012.203-0.28281.23790.0677-0.23750.16130.0804-0.06280.1356-0.1244-0.1337-0.01430.09940.00690.00520.1038-0.02880.05748.0079-8.884218.3874
33.86390.33280.46871.86830.32141.65110.00490.1201-0.1094-0.1305-0.00570.08660.0445-0.0490.00320.10.0125-0.00540.0697-0.01550.0489.4619-15.574911.2098
42.0046-2.99133.33764.9911-2.35156.5244-0.1329-0.0189-0.06790.2377-0.05560.22560.1176-0.19020.22470.1045-0.01740.04650.1278-0.03130.09212.443-1.58964.1196
53.8623.23770.62138.78094.6727.79380.1274-0.22360.17480.3084-0.08250.1172-0.2561-0.2503-0.05240.12430.020.01670.1117-0.01850.070512.92538.03414.067
62.035-0.3015-0.14873.78061.4482.6532-0.043-0.1532-0.1940.0673-0.04110.02840.3780.02130.0710.1407-0.00830.02490.09110.01360.057518.8544-6.1412-3.6842
73.66652.56924.43547.34487.3752.03020.1073-0.1509-0.16850.34740.0049-0.30470.3410.2754-0.06990.1884-0.0295-0.01460.19280.08160.136328.2471-6.34751.7917
83.40110.44490.96652.34050.76863.58780.0129-0.33080.00010.1122-0.18680.18920.0471-0.0590.13310.0861-0.01010.03440.1297-0.01310.087217.22320.07410.1232
93.5812-1.5609-0.63344.54850.95363.5440.10460.08840.1317-0.3183-0.12460.0222-0.1797-0.23750.0130.08550.01130.01220.0710.00790.058418.61513.3143-7.6665
103.50950.50051.83650.9281-0.91322.76660.15250.0866-0.0887-0.09290.0225-0.1031-0.11220.139-0.19340.0915-0.01690.02740.07720.01240.121124.89483.5055-7.8695
116.5797-1.91521.277.2293-0.83473.73840.0579-0.17760.15790.0551-0.0659-0.2592-0.07030.21380.02690.0736-0.0180.0010.14310.02950.145632.37415.4633-2.3411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:31)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 32:68)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 69:106)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 2:10)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 11:20)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 21:31)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 32:47)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 48:68)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 69:83)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 84:94)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 95:106)

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