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- PDB-8vni: A ligand-free crystal structure of mercaptosuccinate dioxygenase -

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Basic information

Entry
Database: PDB / ID: 8vni
TitleA ligand-free crystal structure of mercaptosuccinate dioxygenase
ComponentsMercaptosuccinate dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase / substrate-free / mercaptosuccinate dioxygenase / MSDO
Function / homologyACETATE ION / :
Function and homology information
Biological speciesVariovorax paradoxus B4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsWang, Y. / Ralls, H. / Jordan, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147510 United States
CitationJournal: To Be Published
Title: Crystal structures of mercaptosuccinate dioxygenase
Authors: Wang, Y. / Ralls, H. / Jordan, S.
History
DepositionJan 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mercaptosuccinate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1729
Polymers21,5361
Non-polymers6358
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-33 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.188, 35.312, 72.310
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mercaptosuccinate dioxygenase


Mass: 21536.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus B4 (bacteria) / Gene: JF629_11860 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 264 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.5, 0.2 M lithium sulfate, 30% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 29426 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Χ2: 1.041 / Net I/σ(I): 5.2 / Num. measured all: 187876
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.57-1.64.40.65814350.6830.9010.3530.7520.49798.2
1.6-1.635.20.63114370.7790.9360.2990.7020.51299.5
1.63-1.6660.56514790.8360.9540.2470.6180.536100
1.66-1.696.40.54714630.8650.9630.2320.5960.596100
1.69-1.736.50.45314390.8860.9690.190.4920.63100
1.73-1.776.70.41114750.920.9790.1710.4460.665100
1.77-1.816.70.36114590.9320.9820.150.3920.772100
1.81-1.866.60.31514660.9470.9860.1310.3420.818100
1.86-1.926.30.2814510.9570.9890.120.3050.97100
1.92-1.986.30.2314560.9650.9910.0990.2511.138100
1.98-2.056.30.20614630.9730.9930.0880.2251.215100
2.05-2.136.90.18714650.9810.9950.0760.2021.263100
2.13-2.236.90.16214840.9830.9960.0660.1751.421100
2.23-2.356.90.14114720.9860.9970.0580.1521.416100
2.35-2.496.70.12614690.9890.9970.0520.1361.439100
2.49-2.686.30.11114780.990.9980.0470.1211.514100
2.68-2.956.30.09414900.9920.9980.040.1021.466100
2.95-3.3870.0714910.9960.9990.0280.0761.362100
3.38-4.266.80.0514980.9980.9990.0210.0541.195100
4.26-506.40.04115560.99910.0170.0450.921100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→41.07 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 2009 6.83 %
Rwork0.1586 --
obs0.1601 29413 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 38 256 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071614
X-RAY DIFFRACTIONf_angle_d0.9812194
X-RAY DIFFRACTIONf_dihedral_angle_d7.8242
X-RAY DIFFRACTIONf_chiral_restr0.061236
X-RAY DIFFRACTIONf_plane_restr0.012295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.26181510.22791896X-RAY DIFFRACTION96
1.61-1.650.22741280.20821934X-RAY DIFFRACTION100
1.65-1.70.23331480.2041927X-RAY DIFFRACTION100
1.7-1.750.21511540.19511939X-RAY DIFFRACTION100
1.75-1.820.22021390.17751942X-RAY DIFFRACTION100
1.82-1.890.19891380.17011954X-RAY DIFFRACTION100
1.89-1.970.19491520.15381940X-RAY DIFFRACTION100
1.97-2.080.20161330.16191973X-RAY DIFFRACTION100
2.08-2.210.16551460.15231945X-RAY DIFFRACTION100
2.21-2.380.17791480.14861967X-RAY DIFFRACTION100
2.38-2.620.19121400.15751953X-RAY DIFFRACTION100
2.62-30.16161390.15431996X-RAY DIFFRACTION100
3-3.780.14791450.13181980X-RAY DIFFRACTION100
3.78-41.070.15731480.15252058X-RAY DIFFRACTION100

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