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- PDB-7syb: Crystal Structure of sulfurtransferase (DsrC family protein) from... -

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Basic information

Entry
Database: PDB / ID: 7syb
TitleCrystal Structure of sulfurtransferase (DsrC family protein) from Acinetobacter baumannii
ComponentsSulfurtransferase
KeywordsTRANSFERASE / SSGCID / sulfurtransferase / DsrC family protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologySulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Transferases; Transferring sulfur-containing groups; Sulfurtransferases / transferase activity / cytoplasm / Sulfurtransferase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of sulfurtransferase (DsrC family protein) from Acinetobacter baumannii
Authors: Calhoun, B.M. / Bolejack, M.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfurtransferase


Theoretical massNumber of molelcules
Total (without water)12,7431
Polymers12,7431
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.500, 46.840, 39.480
Angle α, β, γ (deg.)90.000, 108.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sulfurtransferase /


Mass: 12742.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: p60155_2 / Gene: tusE / Plasmid: AcbaC.18888.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: V5VCI8, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: AcbaC.18888.a.B1.PW38910 at 13 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 0.02M Calcium chloride dihydrate, 0.1M Sodium actetate pH 4.6, 30% v/v MPD (JCSG+ A4). Cryo: Direct. Puck: OKJ-1-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 25, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→29.29 Å / Num. obs: 20040 / % possible obs: 99.6 % / Redundancy: 4.074 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 0.941 / Net I/σ(I): 16.25 / Num. measured all: 81639 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.494.0710.5492.8214640.8460.63299.4
1.49-1.534.070.4093.714550.910.47100
1.53-1.574.0840.3214.6713920.9350.36999.6
1.57-1.624.1290.2445.9413650.9670.2899.9
1.62-1.674.0890.2156.6812960.9710.24899.6
1.67-1.734.1160.1628.5112890.9810.18699.9
1.73-1.84.0870.12910.5412360.9870.14999.8
1.8-1.874.1160.10413.0311840.9920.1299.6
1.87-1.964.10.08315.8811350.9930.09599.6
1.96-2.054.0970.06818.8510770.9950.07999.5
2.05-2.164.0930.05522.8910530.9970.06399.7
2.16-2.294.0590.04725.669560.9970.05499.4
2.29-2.454.0570.04327.979410.9970.049100
2.45-2.654.0510.03929.498570.9980.04599.3
2.65-2.94.0530.03731.627780.9980.04399.4
2.9-3.244.0040.03733.457300.9970.04298.9
3.24-3.744.0060.03135.236270.9980.036100
3.74-4.594.0240.0336.415450.9990.03499.8
4.59-6.483.9630.02736.114280.9990.03199.3
6.48-29.293.8020.02436.262320.9990.02996.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX4220refinement
PDB_EXTRACT3.27data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.29 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1684 1913 9.55 %
Rwork0.1387 18121 -
obs0.1416 20034 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.74 Å2 / Biso mean: 20.984 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.45→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 144 970
Biso mean---36.69 -
Num. residues----103
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.45-1.490.24111340.185312761410
1.49-1.530.1941240.149813191443
1.53-1.570.18471400.131612741414
1.57-1.620.17431420.128912931435
1.62-1.680.18861260.12712831409
1.68-1.750.18171360.132512831419
1.75-1.830.19111490.152312751424
1.83-1.920.19561460.139812881434
1.92-2.040.19041280.13313251453
2.04-2.20.17571300.14212821412
2.2-2.420.18311220.137513041426
2.42-2.770.16591440.147913011445
2.77-3.490.16521420.138512931435
3.49-29.290.13491500.131913251475

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