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- PDB-5wa0: Crystal Structure of the sulfite dehydrogenase, SorT R78Q mutant ... -

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Basic information

Entry
Database: PDB / ID: 5wa0
TitleCrystal Structure of the sulfite dehydrogenase, SorT R78Q mutant from Sinorhizobium meliloti
ComponentsPutative sulfite oxidase
KeywordsOXIDOREDUCTASE / sulfite dehydrogenase / METAL BINDING PROTEIN
Function / homology
Function and homology information


sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / heme binding
Similarity search - Function
Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / 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. ...Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM / Sulfite oxidase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMaher, M.J.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions.
Authors: Hsiao, J.C. / McGrath, A.P. / Kielmann, L. / Kalimuthu, P. / Darain, F. / Bernhardt, P.V. / Harmer, J. / Lee, M. / Meyers, K. / Maher, M.J. / Kappler, U.
History
DepositionJun 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sulfite oxidase
B: Putative sulfite oxidase
C: Putative sulfite oxidase
D: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3308
Polymers156,3094
Non-polymers2,0214
Water19,3481074
1
A: Putative sulfite oxidase
B: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1654
Polymers78,1542
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area27470 Å2
MethodPISA
2
C: Putative sulfite oxidase
D: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1654
Polymers78,1542
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-25 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.520, 91.780, 109.670
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative sulfite oxidase


Mass: 39077.152 Da / Num. of mol.: 4 / Fragment: UNP residues 35-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04049 / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: Q92M24, sulfite oxidase
#2: Chemical
ChemComp-MSS / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM


Mass: 505.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12MoN5O7PS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1074 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6
Details: 0.1 M Bis-Tris propane pH 6.0, 0.2 M sodium malonate, 17.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.87
11-h,-k,l20.13
ReflectionResolution: 2.1→50 Å / Num. obs: 95573 / % possible obs: 86.1 % / Redundancy: 2.5 % / Net I/σ(I): 6.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PW3

4pw3


Resolution: 2.1→43.94 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.302 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.053
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 4298 5.1 %RANDOM
Rwork0.2173 ---
obs0.2201 79560 74.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.54 Å2 / Biso mean: 21.686 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--7.74 Å20 Å2-2.57 Å2
2--12.31 Å20 Å2
3----4.56 Å2
Refinement stepCycle: final / Resolution: 2.1→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10928 0 104 1074 12106
Biso mean--16.81 26.34 -
Num. residues----1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911337
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210673
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.96515489
X-RAY DIFFRACTIONr_angle_other_deg0.938324603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45251470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38224.81447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.551151770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0071556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022437
LS refinement shellResolution: 2.1→2.139 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 48 -
Rwork0.213 731 -
all-779 -
obs--9.36 %
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)
11.0583-0.1895-0.07410.2318-0.16581.21110.00790.1106-0.1257-0.0153-0.02590.00210.0985-0.03270.0180.086-0.00950.01710.0147-0.02240.0794-1.181513.5634.3901
20.9450.15230.02580.14520.12481.15030.0127-0.1108-0.09690.0156-0.0220.00230.11730.0350.00930.07980.01840.00740.0220.02610.07222.083513.526263.8541
31.110.0658-0.01150.2920.07731.2025-0.00590.09640.1011-0.02490.00180.0318-0.12430.04780.00410.0803-0.01040.01930.01210.01520.08148.7391-13.6201-8.9805
40.92010.0441-0.01980.181-0.03621.2526-0.0264-0.07670.08160.01380.0127-0.012-0.0989-0.04950.01370.08610.01670.01060.0122-0.01650.079524.8522-14.059620.4746
50.2373-0.12010.03570.2429-0.07721.4962-0.0127-0.07160.05180.00120.00720.0034-0.1043-0.16390.00550.05630.01550.00970.0447-0.01620.0641-9.834423.462254.3853
60.4683-0.147-0.00420.1930.0741.2588-0.04150.06320.0656-0.0110.0009-0.0252-0.13590.16070.04060.0517-0.02720.01870.04810.01240.0730.528523.966944.0272
70.2219-0.0075-0.12830.23070.07791.7577-0.0395-0.0871-0.06330.02040.0122-0.06140.07410.15690.02730.04830.02640.00560.05190.00250.079256.9361-23.885610.8773
80.3283-0.1335-0.06090.06930.06021.8072-0.01070.0556-0.0647-0.0058-0.02050.05750.127-0.09230.03130.0792-0.0338-0.00480.0234-0.0090.085616.7877-24.10650.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 268
2X-RAY DIFFRACTION2B35 - 268
3X-RAY DIFFRACTION3C35 - 268
4X-RAY DIFFRACTION4D35 - 268
5X-RAY DIFFRACTION5A269 - 399
6X-RAY DIFFRACTION6B269 - 399
7X-RAY DIFFRACTION7C269 - 399
8X-RAY DIFFRACTION8D269 - 399

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