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- PDB-6mxv: The crystal structure of a rhodanese-like family protein from Fra... -

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Basic information

Entry
Database: PDB / ID: 6mxv
TitleThe crystal structure of a rhodanese-like family protein from Francisella tularensis subsp. tularensis SCHU S4
ComponentsRhodanese-like family protein
KeywordsUNKNOWN FUNCTION / Rhodanese-like family protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyRhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / DI(HYDROXYETHYL)ETHER / Rhodanese-like family protein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsTan, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of a rhodanese-like family protein from Francisella tularensis subsp. tularensis SCHU S4
Authors: Tan, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodanese-like family protein
B: Rhodanese-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,25311
Polymers57,1032
Non-polymers1,1509
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-21 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.721, 111.108, 50.339
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Rhodanese-like family protein


Mass: 28551.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1127 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5NFU2

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Non-polymers , 6 types, 355 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350 25%, 0.2M MgCl2, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97818 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97818 Å / Relative weight: 1
ReflectionResolution: 1.78→48.6 Å / Num. obs: 50307 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 15.348 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Χ2: 0.756 / Net I/σ(I): 22.3
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 2503 / CC1/2: 0.839 / Rpim(I) all: 0.266 / Rrim(I) all: 0.56 / Χ2: 0.894 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→48.6 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1884 2463 5.02 %
Rwork0.1576 --
obs0.1592 49107 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 75 346 4362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094105
X-RAY DIFFRACTIONf_angle_d0.9585518
X-RAY DIFFRACTIONf_dihedral_angle_d6.8223427
X-RAY DIFFRACTIONf_chiral_restr0.059591
X-RAY DIFFRACTIONf_plane_restr0.005721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7809-1.81510.25951150.20521991X-RAY DIFFRACTION74
1.8151-1.85220.26221620.18442258X-RAY DIFFRACTION86
1.8522-1.89250.221270.17872490X-RAY DIFFRACTION93
1.8925-1.93650.23151370.16772586X-RAY DIFFRACTION96
1.9365-1.98490.19421180.15482600X-RAY DIFFRACTION98
1.9849-2.03860.191330.15512649X-RAY DIFFRACTION97
2.0386-2.09860.18321180.15562677X-RAY DIFFRACTION98
2.0986-2.16630.1991450.14762634X-RAY DIFFRACTION99
2.1663-2.24370.1941650.15642642X-RAY DIFFRACTION99
2.2437-2.33360.18791480.15112670X-RAY DIFFRACTION99
2.3336-2.43980.19091120.15152687X-RAY DIFFRACTION99
2.4398-2.56840.19931310.172638X-RAY DIFFRACTION98
2.5684-2.72930.21271480.16392673X-RAY DIFFRACTION99
2.7293-2.940.22861380.16962685X-RAY DIFFRACTION99
2.94-3.23580.19721610.16852653X-RAY DIFFRACTION99
3.2358-3.70390.15661240.15222699X-RAY DIFFRACTION100
3.7039-4.66590.15211550.13282666X-RAY DIFFRACTION99
4.6659-48.60.16361260.16192746X-RAY DIFFRACTION99
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)
10.9911-0.1317-0.40191.84710.04341.07770.00260.03890.0527-0.11870.021-0.0111-0.0012-0.0134-0.01950.0751-0.0035-0.00430.0870.00860.07610.27236.054431.4184
22.0513.8765-1.67437.4695-3.22751.3811-0.06080.12820.1825-0.34390.23470.3251-0.1807-0.1464-0.17140.21410.0060.01240.1424-0.00660.1408-5.752713.605221.8166
32.01370.20670.91812.24210.07391.7087-0.0009-0.14510.055-0.0698-0.1140.3220.007-0.19070.08230.101-0.00050.01410.1257-0.04920.1428-21.1849-1.382535.339
41.00240.23410.46761.80790.08761.3710.0021-0.0307-0.06980.1009-0.01680.00320.0446-0.0220.02040.0960.00070.01680.09670.00080.0921-0.444710.736844.2685
51.4754-3.60661.63539.2425-4.07961.8095-0.1137-0.0645-0.07280.48440.13950.21860.0038-0.127-0.010.19990.01310.00510.1752-0.0170.1227-7.689833.337653.0145
63.40650.77780.0161.7849-0.41042.0925-0.0384-0.18010.14350.05250.03640.1653-0.0186-0.19690.00250.08650.0159-0.01720.1126-0.01090.1172-21.429848.324837.4245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 252 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 119 )
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 145 )
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 252 )

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