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- PDB-8s5s: Crystal structure of a Sulfite dehydrogenase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 8s5s
TitleCrystal structure of a Sulfite dehydrogenase from Thermus thermophilus
ComponentsPutaitve sulfite oxidase
KeywordsOXIDOREDUCTASE / Electron transfer / SOR / Molybdopterine
Function / homology
Function and homology information


sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / heme binding
Similarity search - Function
Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM / Putaitve sulfite oxidase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDjeghader, A. / Soulimane, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Inorg.Chem. / Year: 2024
Title: Structural and Spectroscopic Investigations of pH-Dependent Mo(V) Species in a Bacterial Sulfite-Oxidizing Enzyme.
Authors: Djeghader, A. / Rendon, J. / Biaso, F. / Gerbaud, G. / Nitschke, W. / Schoepp-Cothenet, B. / Soulimane, T. / Grimaldi, S.
#1: Journal: Chem Commun (Camb) / Year: 2020
Title: Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase.
Authors: Djeghader, A. / Rossotti, M. / Abdulkarim, S. / Biaso, F. / Gerbaud, G. / Nitschke, W. / Schoepp-Cothenet, B. / Soulimane, T. / Grimaldi, S.
History
DepositionFeb 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putaitve sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6973
Polymers43,1561
Non-polymers5412
Water5,747319
1
A: Putaitve sulfite oxidase
hetero molecules

A: Putaitve sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3946
Polymers86,3122
Non-polymers1,0814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5700 Å2
ΔGint-65 kcal/mol
Surface area28910 Å2
Unit cell
Length a, b, c (Å)130.020, 130.020, 114.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-684-

HOH

31A-689-

HOH

41A-697-

HOH

51A-761-

HOH

61A-765-

HOH

71A-767-

HOH

81A-789-

HOH

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Components

#1: Protein Putaitve sulfite oxidase


Mass: 43156.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1325 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SIP4
#2: Chemical ChemComp-MSS / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM


Mass: 505.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12MoN5O7PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 14% PEG 8000, 0.1 M sodium citrate tribasic dihydrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96851 Å / Relative weight: 1
ReflectionResolution: 1.85→42.56 Å / Num. obs: 49202 / % possible obs: 99.94 % / Redundancy: 12.2 % / Biso Wilson estimate: 31.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.02516 / Net I/σ(I): 16.83
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 4833 / CC1/2: 0.733 / CC star: 0.92 / Rpim(I) all: 0.3857 / % possible all: 99.96

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.559 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.594 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.192 2000 4.065 %
Rwork0.1653 47202 -
all0.166 --
obs-49202 99.961 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.295 Å2-0.147 Å2-0 Å2
2---0.295 Å2-0 Å2
3---0.956 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 27 319 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162956
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.8474259
X-RAY DIFFRACTIONr_angle_other_deg0.6171.7486797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.001524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84810494
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.003101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.56710142
X-RAY DIFFRACTIONr_chiral_restr0.0930.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02744
X-RAY DIFFRACTIONr_nbd_refined0.2150.2530
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22773
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21516
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21693
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0750.222
X-RAY DIFFRACTIONr_nbd_other0.1360.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.241
X-RAY DIFFRACTIONr_mcbond_it3.0223.2611523
X-RAY DIFFRACTIONr_mcbond_other3.0213.2611523
X-RAY DIFFRACTIONr_mcangle_it3.845.8431905
X-RAY DIFFRACTIONr_mcangle_other3.855.8451906
X-RAY DIFFRACTIONr_scbond_it4.9213.8181592
X-RAY DIFFRACTIONr_scbond_other4.9193.8181593
X-RAY DIFFRACTIONr_scangle_it7.3466.7432348
X-RAY DIFFRACTIONr_scangle_other7.3456.7432349
X-RAY DIFFRACTIONr_lrange_it8.60831.943496
X-RAY DIFFRACTIONr_lrange_other8.59231.0093421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.2951440.26534050.26635500.9350.95299.97180.252
1.898-1.950.2471420.23233580.23335000.9540.9591000.217
1.95-2.0060.2471380.22132400.22233780.960.9651000.2
2.006-2.0680.2671340.21331630.21632970.9480.9681000.19
2.068-2.1360.2181300.18430680.18531980.9680.9761000.16
2.136-2.210.2151260.17529800.17631060.9670.9791000.152
2.21-2.2930.2161220.17328700.17529920.9670.981000.15
2.293-2.3870.2121170.17227670.17428840.9710.9811000.148
2.387-2.4930.2111130.16126710.16327840.9670.9831000.14
2.493-2.6140.2081080.1625430.16226510.9730.9841000.14
2.614-2.7550.2091040.1624450.16225490.970.9841000.143
2.755-2.9210.185970.15422950.15523920.9740.9851000.141
2.921-3.1220.211920.16621890.16822810.9730.9821000.156
3.122-3.370.175870.15820350.15921240.9810.98599.90580.155
3.37-3.690.159800.15918890.15919690.9830.9861000.16
3.69-4.1210.167720.14717270.14817990.9860.9881000.154
4.121-4.7510.15650.1315220.13115880.9880.9999.9370.145
4.751-5.8010.167570.14113230.14213820.9880.9999.85530.159
5.801-8.1290.21440.17710590.17811030.9750.9851000.205
8.129-42.5590.173280.1996520.1986850.9810.97199.27010.233

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