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- PDB-2ypm: Crystal Structure of Ancestral Thioredoxin Relative to Last Anima... -

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Basic information

Entry
Database: PDB / ID: 2ypm
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Animal and Fungi Common Ancestor (LAFCA) from the Precambrian Period
ComponentsLAFCA THIOREDOXIN
KeywordsOXIDOREDUCTASE / ANCESTRAL RECONSTRUCTED
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 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 30, 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: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAFCA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,9071
Polymers11,9071
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.493, 42.791, 55.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LAFCA THIOREDOXIN


Mass: 11906.608 Da / Num. of mol.: 1
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: thioredoxin-disulfide reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsANCESTRAL RECONSTRUCTED

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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: 1.95 Å3/Da / Density % sol: 36.82 % / Description: NONE
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 5.5
Details: COUNTER-DIFFUSION: 0.1M TRIS-HCL, 30% PEG 4000, 0.2 M MGCL2, PH 8.50, T 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 4904 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 10.4 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.26
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERV

1erv


Resolution: 2.199→19.983 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 227 4.7 %
Rwork0.1666 --
obs0.1701 4874 99.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.384 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--1.5204 Å20 Å20 Å2
2---1.2767 Å20 Å2
3---2.7972 Å2
Refinement stepCycle: LAST / Resolution: 2.199→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 52 862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008888
X-RAY DIFFRACTIONf_angle_d1.0871204
X-RAY DIFFRACTIONf_dihedral_angle_d15.476343
X-RAY DIFFRACTIONf_chiral_restr0.075136
X-RAY DIFFRACTIONf_plane_restr0.005156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1985-2.76870.30691090.1942253X-RAY DIFFRACTION99
2.7687-19.98360.2141180.15652394X-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)
15.66530.6083-0.7412.2074-0.02333.3390.26770.56720.0979-0.7711-0.1180.43470.1099-0.31140.18820.24580.0887-0.12490.1189-0.03710.194-22.74383.63814.2795
23.9217-0.35550.25853.1358-0.12963.0976-0.0276-0.00020.1110.06520.2342-0.3422-0.35120.36380.01260.1389-0.0320.03930.0952-0.07890.1047-12.8836-1.065511.2743
31.6762-0.429-2.05530.96791.37113.3513-0.08830.4977-0.1872-0.2107-0.12120.57-0.0102-0.77810.06930.1296-0.0509-0.08960.36710.0670.4586-29.0725-4.192111.2887
42.6110.93370.1271.29730.34441.1981-0.01020.17490.0159-0.18080.19390.2640.0863-0.0986-0.00920.1262-0.16880.05490.1222-0.0210.173-19.4881-8.10235.2875
50.35250.34780.47290.7886-1.25427.3101-0.21920.2319-0.2375-0.23990.0084-0.28270.50740.02140.00550.1406-0.06890.10280.1314-0.05770.2011-13.948-11.28775.2607
62.26210.247-2.01012.98850.05794.8619-0.1103-0.0505-0.1245-0.18950.2461-0.675-0.11390.4501-0.1330.1279-0.04620.09290.1422-0.09380.3324-5.1826-8.44927.2397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:17)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 18:58)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 59:66)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 67:83)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 84:93)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 94:105)

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