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- PDB-2ynx: Crystal Structure of Ancestral Thioredoxin Relative to Last Archa... -

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Basic information

Entry
Database: PDB / ID: 2ynx
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (LACA) from the Precambrian Period
ComponentsLACA 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: 1.749 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 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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_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 / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: LACA THIOREDOXIN
B: LACA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1484
Polymers24,0662
Non-polymers822
Water3,315184
1
A: LACA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,0331
Polymers12,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LACA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1153
Polymers12,0331
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.153, 36.294, 48.118
Angle α, β, γ (deg.)90.76, 107.97, 111.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LACA THIOREDOXIN


Mass: 12033.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OXIDOREDUCTASE, ANCESTRAL RECONSTRUCTED / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.6 % / Description: NONE
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 9
Details: COUNTER-DIFFUSION: TRIS-HCL 0.1M, 20% PEG 400, 15% PEG 4000, 10% PEG 8000; PH 9.0, 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.75→45.32 Å / Num. obs: 18887 / % possible obs: 97.6 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 88.7

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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: 1.749→45.322 Å / SU ML: 0.25 / σ(F): 1.97 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 969 5.1 %
Rwork0.1603 --
obs0.1631 18885 97.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.652 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.4954 Å20.4176 Å2-3.187 Å2
2--2.083 Å2-1.2278 Å2
3----0.5877 Å2
Refinement stepCycle: LAST / Resolution: 1.749→45.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 5 184 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131874
X-RAY DIFFRACTIONf_angle_d1.3872553
X-RAY DIFFRACTIONf_dihedral_angle_d12.967750
X-RAY DIFFRACTIONf_chiral_restr0.088282
X-RAY DIFFRACTIONf_plane_restr0.008333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7488-1.8410.32081420.24632310X-RAY DIFFRACTION88
1.841-1.95630.23161270.17442604X-RAY DIFFRACTION98
1.9563-2.10740.21061590.15522559X-RAY DIFFRACTION99
2.1074-2.31940.2331410.14332595X-RAY DIFFRACTION99
2.3194-2.6550.19691200.14672626X-RAY DIFFRACTION99
2.655-3.34490.2131460.14832603X-RAY DIFFRACTION100
3.3449-45.33740.19941340.16482619X-RAY DIFFRACTION100
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)
14.66314.34620.17564.71150.90113.91330.1059-0.15110.21510.3465-0.20790.2695-0.0506-0.08190.05050.27710.0609-0.02690.1143-0.05590.1168-7.77915.0878-0.2102
21.47290.06841.53381.1646-0.2773.38490.0186-0.17-0.0010.36610.1111-0.1521-0.0174-0.056-0.00890.16450.0273-0.03560.0824-0.02610.0875-2.34020.8802-3.4017
32.9092-2.07162.97694.7334-4.16954.3667-0.0195-0.1778-0.1080.17090.15690.2272-0.0328-0.3046-0.1160.1004-0.0130.03910.123-0.0020.103-11.0155-9.1171-8.9943
41.1777-1.03670.544.8796-2.81382.7524-0.0544-0.14170.13880.13750.07240.0807-0.118-0.0785-0.00550.12740.00150.0170.0835-0.03910.0818-5.11352.1219-5.9134
51.7503-0.2327-0.02523.2837-0.83071.8037-0.0016-0.150.08520.0939-0.0727-0.2871-0.00140.17210.11110.0683-0.00570.00740.0886-0.00340.10591.2699-1.5094-11.9983
64.27550.10171.7934.2879-0.21774.13590.0175-0.1914-0.20660.1348-0.102-0.38490.37090.12850.07130.14760.0190.02780.11770.0370.09232.6114-13.1355-8.2554
74.9448-0.27220.13955.5204-0.27554.4180.0290.31660.3476-0.31230.0261-0.0748-0.2321-0.0238-0.05450.1637-0.02120.04950.16120.02660.06396.1441-6.8632-35.7565
80.26370.71090.87675.98180.10894.1644-0.06180.24820.0409-0.69650.0990.10680.0466-0.3472-0.00810.19670.04120.00890.42910.02450.1117-6.029-9.7775-35.8303
91.88630.23650.4471.02080.14131.25580.0917-0.1491-0.1118-0.05010.0314-0.0438-0.03930.0321-0.07780.0283-0.00840.02180.0851-0.00540.07868.4834-13.7418-27.1755
101.0893-0.6370.30412.36220.12520.94530.0722-0.0479-0.18010.01230.0786-0.00830.1636-0.0393-0.01520.0393-0.0155-0.00090.05280.0310.08330.2005-19.9112-22.4597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:9)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 10:30)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 31:46)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 47:67)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 68:93)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 94:105)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 1:14)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 15:19)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 20:82)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 83:105)

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