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- PDB-6esx: Caulobacter crescentus Trx1 -

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Basic information

Entry
Database: PDB / ID: 6esx
TitleCaulobacter crescentus Trx1
ComponentsThioredoxin 1
KeywordsCELL CYCLE / Thioredoxin / CCNA_03653 / Trx1 / ClpXP / redox
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaulobacter crescentus NA1000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å
AuthorsVan Molle, I. / Wahni, K. / Goemans, C.V. / Beaufay, F. / Collet, J.F. / Messens, J.
Funding support Belgium, 4items
OrganizationGrant numberCountry
FRIA Belgium
VIB Marie Curie COFUND Belgium
Hercules foundationHERC16 Belgium
VUBSRP34 Belgium
CitationJournal: J. Biol. Chem. / Year: 2018
Title: An essential thioredoxin is involved in the control of the cell cycle in the bacterium
Authors: Goemans, C.V. / Beaufay, F. / Wahni, K. / Van Molle, I. / Messens, J. / Collet, J.F.
History
DepositionOct 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
C: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)39,2073
Polymers39,2073
Non-polymers00
Water48627
1
A: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)13,0691
Polymers13,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)13,0691
Polymers13,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)13,0691
Polymers13,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.100, 85.100, 105.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Thioredoxin 1 /


Mass: 13068.991 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus NA1000 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3CDN9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6; 20% 2-propanol; 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.797→42.862 Å / Num. obs: 10727 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rrim(I) all: 0.166 / Net I/σ(I): 2.1
Reflection shellResolution: 2.797→2.97 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1732 / Rrim(I) all: 1.12 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i4a

2i4a


Resolution: 2.797→42.862 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.65
RfactorNum. reflection% reflection
Rfree0.2702 537 5.01 %
Rwork0.1876 --
obs0.1916 10727 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.797→42.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 0 27 2408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092447
X-RAY DIFFRACTIONf_angle_d1.2163358
X-RAY DIFFRACTIONf_dihedral_angle_d15.2171489
X-RAY DIFFRACTIONf_chiral_restr0.062413
X-RAY DIFFRACTIONf_plane_restr0.012423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7967-3.07810.34461330.28332533X-RAY DIFFRACTION99
3.0781-3.52340.31711340.20682539X-RAY DIFFRACTION100
3.5234-4.43830.25091330.15452547X-RAY DIFFRACTION100
4.4383-42.86740.20831370.15952571X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.4014 Å / Origin y: 42.77 Å / Origin z: 61.7122 Å
111213212223313233
T0.1101 Å20.0522 Å2-0.02 Å2-0.1485 Å2-0.0373 Å2--0.1404 Å2
L0.1919 °20.0787 °20.1434 °2-0.0868 °2-0.0225 °2--0.2432 °2
S0.0512 Å °-0.035 Å °-0.0687 Å °0.0243 Å °-0.0616 Å °-0.0033 Å °-0.0721 Å °0.0263 Å °0.0112 Å °
Refinement TLS groupSelection details: all

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