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- PDB-9edl: Crystal structure of Francisella tularensis DsbA1 -

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Basic information

Entry
Database: PDB / ID: 9edl
TitleCrystal structure of Francisella tularensis DsbA1
ComponentsConserved hypothetical lipoprotein
KeywordsOXIDOREDUCTASE / DsbA / Thioredoxin-like protein / Francisella tularensis
Function / homologyThioredoxin / Thioredoxin-like fold / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / DI(HYDROXYETHYL)ETHER / Conserved hypothetical lipoprotein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis SCHU S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPenning, S. / Heras, B. / Paxman, J.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210100673 Australia
CitationJournal: Comput Struct Biotechnol J / Year: 2024
Title: Unveiling the versatility of the thioredoxin framework: Insights from the structural examination of Francisella tularensis DsbA1.
Authors: Penning, S. / Hong, Y. / Cunliffe, T. / Hor, L. / Totsika, M. / Paxman, J.J. / Heras, B.
History
DepositionNov 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical lipoprotein
B: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2059
Polymers51,7062
Non-polymers4997
Water4,792266
1
A: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1565
Polymers25,8531
Non-polymers3024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0494
Polymers25,8531
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.744, 57.275, 168.809
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 Conserved hypothetical lipoprotein


Mass: 25853.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria)
Gene: FTT_0507 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 (C43) / References: UniProt: Q5NHF0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.58), 0.01 mM ZnCl2 and 20% PEG 3350 (v/v), and protein at 58 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.95→47.39 Å / Num. obs: 31035 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.058 / Rrim(I) all: 0.123 / Net I/σ(I): 8.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.685 / Num. unique obs: 3729 / CC1/2: 0.802 / Rpim(I) all: 0.364 / Rrim(I) all: 0.778 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→42.2 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1560 5.04 %
Rwork0.1836 --
obs0.1857 30927 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 13 266 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006404
X-RAY DIFFRACTIONf_angle_d0.73411
X-RAY DIFFRACTIONf_dihedral_angle_d16.7031326
X-RAY DIFFRACTIONf_chiral_restr0.049553
X-RAY DIFFRACTIONf_plane_restr0.006635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.030.28431150.26142423X-RAY DIFFRACTION92
2.03-2.10.32661290.24012656X-RAY DIFFRACTION100
2.1-2.180.23571520.21292658X-RAY DIFFRACTION100
2.18-2.280.25311290.2022621X-RAY DIFFRACTION99
2.28-2.40.26021640.20242650X-RAY DIFFRACTION100
2.4-2.550.24111500.18862661X-RAY DIFFRACTION100
2.55-2.750.26091350.19622691X-RAY DIFFRACTION100
2.75-3.030.25491390.1972675X-RAY DIFFRACTION100
3.03-3.460.20851250.18262724X-RAY DIFFRACTION100
3.46-4.360.19551500.14982755X-RAY DIFFRACTION100
4.36-100.19581720.1682853X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.319 Å / Origin y: -8.1251 Å / Origin z: 22.4748 Å
111213212223313233
T0.1402 Å20.0143 Å2-0.0032 Å2-0.181 Å2-0.0159 Å2--0.1785 Å2
L0.1112 °20.1125 °2-0.0877 °2-1.1981 °2-0.8335 °2--1.245 °2
S0.0204 Å °0.0048 Å °-0.0039 Å °-0.1521 Å °-0.0333 Å °-0.0091 Å °0.0669 Å °0.0249 Å °0.0075 Å °
Refinement TLS groupSelection details: all

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