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- PDB-8tfs: Crystal structure of the Rhodanese-like domain of Vretifemale_108... -

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Basic information

Entry
Database: PDB / ID: 8tfs
TitleCrystal structure of the Rhodanese-like domain of Vretifemale_1082 from Volvox reticuliferus
ComponentsRhodanese domain-containing protein
KeywordsTRANSFERASE / Rhodanese / sulfur transferase
Function / homologyCalcium sensing receptor, plant / de-etiolation / regulation of stomatal closure / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / cellular response to calcium ion / Rhodanese domain-containing protein
Function and homology information
Biological speciesVolvox reticuliferus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsArbing, M.A. / Jonikas, M. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: To Be Published
Title: Crystal structure of the Rhodanese-like domain of Vretifemale_1082 from Volvox reticuliferus
Authors: Arbing, M.A. / Jonikas, M. / Yeates, T.O.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodanese domain-containing protein
B: Rhodanese domain-containing protein


Theoretical massNumber of molelcules
Total (without water)40,0512
Polymers40,0512
Non-polymers00
Water2,774154
1
A: Rhodanese domain-containing protein


Theoretical massNumber of molelcules
Total (without water)20,0261
Polymers20,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rhodanese domain-containing protein


Theoretical massNumber of molelcules
Total (without water)20,0261
Polymers20,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.390, 66.390, 141.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Rhodanese domain-containing protein


Mass: 20025.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Volvox reticuliferus (plant) / Gene: Vretifemale_1082 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8J4BWA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10% PEG3350. Cryoprotectant: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 23% PEG3350, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.72932 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 1.95→57.5 Å / Num. obs: 50761 / % possible obs: 99.88 % / Redundancy: 9.8 % / Biso Wilson estimate: 40.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08409 / Rpim(I) all: 0.02846 / Rrim(I) all: 0.08888 / Net I/σ(I): 14.03
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.8456 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 2645 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.2763 / Rrim(I) all: 0.8902 / % possible all: 99.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→53.26 Å / SU ML: 0.2475 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 2702 10 %
Rwork0.1854 24318 -
obs0.1879 27020 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→53.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 0 154 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052132
X-RAY DIFFRACTIONf_angle_d0.90412889
X-RAY DIFFRACTIONf_chiral_restr0.0606340
X-RAY DIFFRACTIONf_plane_restr0.0105375
X-RAY DIFFRACTIONf_dihedral_angle_d4.9987306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.34081360.32161229X-RAY DIFFRACTION99.64
1.99-2.020.29751410.28161267X-RAY DIFFRACTION99.93
2.02-2.070.29571400.24531258X-RAY DIFFRACTION99.64
2.07-2.110.29861380.23061237X-RAY DIFFRACTION99.71
2.11-2.160.29521400.19861256X-RAY DIFFRACTION99.93
2.16-2.210.2531440.19511292X-RAY DIFFRACTION99.86
2.21-2.270.24711370.2051240X-RAY DIFFRACTION100
2.27-2.340.23461400.20751262X-RAY DIFFRACTION99.72
2.34-2.420.27951400.22571266X-RAY DIFFRACTION99.93
2.42-2.50.24861420.22041286X-RAY DIFFRACTION99.93
2.5-2.60.22821410.20391268X-RAY DIFFRACTION100
2.6-2.720.24671420.20231272X-RAY DIFFRACTION100
2.72-2.860.22941420.20781281X-RAY DIFFRACTION100
2.86-3.040.24981430.20921282X-RAY DIFFRACTION99.93
3.04-3.280.22481420.21811285X-RAY DIFFRACTION100
3.28-3.610.23231440.19351294X-RAY DIFFRACTION99.93
3.61-4.130.18241460.16581314X-RAY DIFFRACTION99.86
4.13-5.20.1431470.13921324X-RAY DIFFRACTION100
5.21-53.260.18011570.15891405X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -12.8609050956 Å / Origin y: -1.60037038005 Å / Origin z: 12.8250411556 Å
111213212223313233
T0.442734426492 Å20.129275132148 Å20.0540123684855 Å2-0.378024672534 Å20.0442391593988 Å2--0.425643598818 Å2
L1.57669788765 °2-2.22332219363 °20.223498734656 °2-3.45384575384 °20.357827121131 °2--0.0748777253294 °2
S-0.0679373078141 Å °-0.0180198015796 Å °0.0712720376385 Å °0.142620147773 Å °0.03903718979 Å °0.0913417811601 Å °-0.0246795025476 Å °-0.022999066054 Å °0.0253293559496 Å °
Refinement TLS groupSelection details: all

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