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- PDB-7ool: Crystal structure of a Candidatus photodesmus katoptron thioredox... -

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Basic information

Entry
Database: PDB / ID: 7ool
TitleCrystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / QUIMERA FROM ANCESTRAL LPBCA
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Thioredoxin
Similarity search - Component
Biological speciesCandidatus Photodesmus katoptron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsGavira, J.A. / Ibarra-Molero, B. / Gamiz-Arco, G. / Risso, V. / Sanchez-Ruiz, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-097142-B-100 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression.
Authors: Gamiz-Arco, G. / Risso, V.A. / Gaucher, E.A. / Gavira, J.A. / Naganathan, A.N. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,09311
Polymers24,1182
Non-polymers9759
Water21612
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7307
Polymers12,0591
Non-polymers6716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3634
Polymers12,0591
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.080, 140.080, 140.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-306-

SO4

21A-401-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 71 or resid 73...
d_2ens_1(chain "B" and (resid 2 through 71 or resid 73...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSILEA1 - 70
d_12ens_1SERGLYA72 - 82
d_13ens_1VALARGA84 - 98
d_14ens_1PHELEUA100 - 105
d_21ens_1LYSILEB2 - 71
d_22ens_1SERGLYB73 - 83
d_23ens_1VALARGB85 - 99
d_24ens_1PHELEUB101 - 106

NCS oper: (Code: givenMatrix: (-0.984762654858, 0.145034824115, 0.0959552676601), (0.151766602828, 0.447338881635, 0.881393682326), (0.0849082555702, 0.882526387578, -0.462534067248)Vector: 8. ...NCS oper: (Code: given
Matrix: (-0.984762654858, 0.145034824115, 0.0959552676601), (0.151766602828, 0.447338881635, 0.881393682326), (0.0849082555702, 0.882526387578, -0.462534067248)
Vector: 8.04048187856, -33.1379970876, 53.3593898357)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin


Mass: 12059.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Photodesmus katoptron (bacteria)
Gene: trx, O1U_0791 / Variant: Akat1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S3DGC4

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Non-polymers , 7 types, 21 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.71 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HAMPTON RESEARCH: HRI: C33 & C34 PEG-ION: C13 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.85→44.33 Å / Num. obs: 19411 / % possible obs: 99.48 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 82.2 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Net I/σ(I): 7.67
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1077 / CC1/2: 0.454 / CC star: 0.79 / Rpim(I) all: 0.557 / % possible all: 99.91

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.582
Highest resolutionLowest resolution
Rotation44.3 Å2.92 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX

2trx


Resolution: 2.85→44.3 Å / SU ML: 0.5691 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 32.7486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 962 4.96 %
Rwork0.2613 18449 -
obs0.2627 19411 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.61 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 63 12 1723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341761
X-RAY DIFFRACTIONf_angle_d0.68852372
X-RAY DIFFRACTIONf_chiral_restr0.0467281
X-RAY DIFFRACTIONf_plane_restr0.0042288
X-RAY DIFFRACTIONf_dihedral_angle_d10.9236252
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.765195382018 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.4821430.49182673X-RAY DIFFRACTION93.99
3-3.190.35671360.34592629X-RAY DIFFRACTION92.47
3.19-3.430.36851330.29672566X-RAY DIFFRACTION92.12
3.44-3.780.32911400.27322652X-RAY DIFFRACTION94.01
3.78-4.330.25651320.23552620X-RAY DIFFRACTION93.22
4.33-5.440.24191420.21292649X-RAY DIFFRACTION93.97
5.45-44.30.25881360.25342660X-RAY DIFFRACTION94.11
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)
14.397419554490.433026640733-1.199670698183.53814970942-1.35973111873.973802490330.0765729870276-0.1622177231210.1860340811080.07901766064380.2096062442370.106717047943-0.247470738685-0.121069771745-0.0002866876077940.5983201192240.02185617144060.02134222043360.5764807370370.04265359001620.5375002110210.894379856920.48420725834.6059510092
24.17666864417-0.8808266155050.2994531703972.17580737729-0.3524261143033.91798781973-0.119041030705-0.5558273634330.00591647267480.3086718138550.0148593656387-0.0219774615113-0.4910661725250.1948802152660.0004531239669280.7786476392350.02432204036890.05598500156340.6890698812640.05804930558610.5904769449743.613437504638.2589526111655.958346511
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1 - 106

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 2 through 107)AA2 - 107
22(chain 'B' and resid 1 through 106)BB1 - 106

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