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- PDB-4ba7: Crystal Structure of Ancestral Thioredoxin Relative to Last Bacte... -

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Basic information

Entry
Database: PDB / ID: 4ba7
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Bacteria Common Ancestor (LBCA) from the Precambrian Period
ComponentsLBCA THIOREDOXIN
KeywordsOXIDOREDUCTASE
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionSep 12, 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: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
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 / _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 2.1Nov 20, 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: LBCA THIOREDOXIN
B: LBCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2444
Polymers24,1202
Non-polymers1242
Water1,24369
1
A: LBCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1222
Polymers12,0601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LBCA THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1222
Polymers12,0601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.701, 192.701, 192.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11B-2030-

HOH

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Components

#1: Protein LBCA THIOREDOXIN


Mass: 12059.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET30A PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: EC: 4.7.1.4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.51 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 293 K / pH: 3
Details: COUNTERDIFFUSION METHOD 15% PEG 1500, 0.01 M CITRIC ACID, PH 3.0, 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973
DetectorType: ADSC QUANTUM 315 / 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: 2.45→58.1 Å / Num. obs: 11808 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 36.71 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

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

2trx


Resolution: 2.45→58.102 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 582 4.9 %
Rwork0.1604 --
obs0.1629 11799 99.83 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.364 Å2 / ksol: 0.7 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.45→58.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 8 69 1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151880
X-RAY DIFFRACTIONf_angle_d1.4742559
X-RAY DIFFRACTIONf_dihedral_angle_d13.985759
X-RAY DIFFRACTIONf_chiral_restr0.077280
X-RAY DIFFRACTIONf_plane_restr0.007338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4505-2.69710.25031400.16822722X-RAY DIFFRACTION100
2.6971-3.08730.22651580.16872734X-RAY DIFFRACTION100
3.0873-3.88960.18551600.1442770X-RAY DIFFRACTION100
3.8896-58.11780.21221240.16592991X-RAY DIFFRACTION99
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)
15.70912.27811.49776.00490.79055.88960.1347-0.8143-0.50280.7625-0.1077-0.29110.37030.33-0.19770.39950.0023-0.02210.45910.00460.379418.850354.550522.1094
22.7761-0.87390.90951.81050.0143.4920.29690.1653-0.1574-0.2864-0.0131-0.10030.03020.1684-0.31670.3076-0.0530.0130.2324-0.05920.321716.311856.79076.7705
36.7678-0.91740.00632.54660.18722.58510.0404-0.34270.37080.4110.0055-0.14420.0121-0.0442-0.09450.2527-0.06660.00120.2271-0.06370.250615.802556.836416.3838
43.91280.61141.88212.07340.90434.6095-0.21230.0340.8234-0.13450.081-0.247-1.43770.27720.19630.4404-0.10650.04330.2347-0.0370.462215.609866.311613.6136
56.52042.73842.40234.56432.25733.6270.46850.04270.7540.3589-0.37220.066-0.8570.54790.0230.8464-0.45970.12710.64880.00820.577526.31567.57517.5931
63.0248-3.15950.8098.84123.02523.02920.36030.14510.7385-0.3815-0.4572-0.7458-0.95650.32120.12320.3552-0.01740.03330.324-0.00210.418822.989345.5369.3531
76.5205-1.35811.94383.7668-1.35266.64070.0369-0.36570.1977-0.1287-0.2028-0.50790.04340.42680.23290.21960.02270.04270.21810.03320.282921.712639.708510.6792
88.33780.06913.41764.97710.33496.1944-0.4197-0.53870.11070.48130.07360.096-0.5874-0.09680.27910.2953-0.0129-0.0010.34270.04560.343612.075940.875419.5989
92.55960.23712.33853.7022-0.84762.44320.050.3335-0.3253-0.42340.0162-0.3128-0.00060.4732-0.00340.30870.02360.09920.25560.00550.383220.263139.49315.0998
106.8839-0.3191-0.5983.58140.27543.44770.0899-0.2131-0.82350.0313-0.0503-0.09940.72420.1977-0.12450.38810.03860.0020.17350.05410.342217.435331.002310.3704
115.3283-0.0111.45874.927-0.46343.596-0.7015-0.3137-0.5423-0.1912-0.5186-0.48061.17650.8632-0.19520.77270.05040.32510.55980.35630.632314.738429.639123.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:20)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 21:47)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 48:69)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 70:94)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 95:106)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 2:10)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 11:31)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 32:52)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 53:69)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 70:94)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 95:106)

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