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- PDB-4pw3: Crystal structure of the sulfite dehydrogenase SorT from Sinorhiz... -

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Basic information

Entry
Database: PDB / ID: 4pw3
TitleCrystal structure of the sulfite dehydrogenase SorT from Sinorhizobium meliloti
ComponentsPutative sulfite oxidase
KeywordsOXIDOREDUCTASE / SULFITE OXIDASE / SULFITE DEHYDROGENASE / MOLYBDOPTERIN
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 speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMcGrath, A.P. / Maher, M.J.
CitationJournal: Elife / Year: 2015
Title: Structural basis of interprotein electron transfer in bacterial sulfite oxidation.
Authors: McGrath, A.P. / Laming, E.L. / Casas Garcia, G.P. / Kvansakul, M. / Guss, J.M. / Trewhella, J. / Calmes, B. / Bernhardt, P.V. / Hanson, G.R. / Kappler, U. / Maher, M.J.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)160,35610
Polymers158,2114
Non-polymers2,1456
Water6,774376
1
A: Putative sulfite oxidase
B: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1785
Polymers79,1052
Non-polymers1,0733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-19 kcal/mol
Surface area27170 Å2
MethodPISA
2
C: Putative sulfite oxidase
D: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1785
Polymers79,1052
Non-polymers1,0733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-19 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.064, 92.225, 109.433
Angle α, β, γ (deg.)90.00, 89.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
Putative sulfite oxidase


Mass: 39552.684 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 32-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02832, SMc04049 / Plasmid: PPROEXSMC4049 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 8% ETHYLENE GLYCOL, 0.1M MANGANESE (II) CHLORIDE TETRAHYDRATE, 17.5% PEG 10000 , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: SI VORTEX ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.495
11-h,-k,l20.505
ReflectionResolution: 2.35→50 Å / Num. obs: 77971 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 5.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.669 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BPB

2bpb


Resolution: 2.35→47.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.881 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3927 5 %RANDOM
Rwork0.208 ---
obs0.21 77951 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.46 Å2
Baniso -1Baniso -2Baniso -3
1--29.54 Å20 Å2-0.85 Å2
2--56.88 Å20 Å2
3----27.34 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10890 0 112 376 11378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211255
X-RAY DIFFRACTIONr_bond_other_d0.0030.027383
X-RAY DIFFRACTIONr_angle_refined_deg1.061.96915375
X-RAY DIFFRACTIONr_angle_other_deg0.86318101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25351454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87424.596433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.403151740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5461557
X-RAY DIFFRACTIONr_chiral_restr0.0690.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022119
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4521.57221
X-RAY DIFFRACTIONr_mcbond_other0.0441.52981
X-RAY DIFFRACTIONr_mcangle_it0.854211599
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.98834034
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7344.53776
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4499 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.03 Å

Dom-IDAuth asym-IDTypeWeight position
1Atight positional0.05
2Btight positional0.05
3Ctight positional0.05
4Dtight positional0.05
1Atight thermal0.5
2Btight thermal0.5
3Ctight thermal0.5
4Dtight thermal0.5
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 251 -
Rwork0.316 4605 -
obs--82.92 %

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