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- PDB-2ca3: Sulfite dehydrogenase from Starkeya Novella r55m mutant -

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Basic information

Entry
Database: PDB / ID: 2ca3
TitleSulfite dehydrogenase from Starkeya Novella r55m mutant
Components(SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE / SULFITE OXIDASE / MOLYBDOPTERIN / C-TYPE CYTOCHROME / HEME / MUTANT
Function / homology
Function and homology information


molybdenum ion binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion 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 / Cytochrome c-like domain ...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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEME C / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM / Sulfite:cytochrome c oxidoreductase subunit B / Sulfite:cytochrome c oxidoreductase subunit A
Similarity search - Component
Biological speciesTHIOBACILLUS NOVELLUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBailey, S. / Kappler, U. / Feng, C. / Honeychurch, M.J. / Bernhardt, P.V. / Tollin, G. / Enemark, J.H.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Molecular basis for enzymatic sulfite oxidation: how three conserved active site residues shape enzyme activity.
Authors: Bailey, S. / Rapson, T. / Johnson-Winters, K. / Astashkin, A.V. / Enemark, J.H. / Kappler, U.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidizing Enzymes is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and ...Title: Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidizing Enzymes is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and a C-Type Cytochrome Subunit
Authors: Kappler, U. / Bailey, S.
History
DepositionDec 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_status ...citation / pdbx_database_status / reflns / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 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 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT A
B: SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3296
Polymers49,0142
Non-polymers1,3164
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-81.22 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.654, 93.321, 56.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT ... , 2 types, 2 molecules AB

#1: Protein SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT A


Mass: 40168.723 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS NOVELLUS (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA16
#2: Protein SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT B


Mass: 8844.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS NOVELLUS (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA15

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Non-polymers , 4 types, 358 molecules

#3: Chemical ChemComp-MSS / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM


Mass: 505.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12MoN5O7PS2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 87 TO MET
Has protein modificationY
Sequence detailsTHE TRANSLATED SEQUENCES FOR CHAINS A AND B INCLUDE SIGNAL PEPTIDES WHICH ARE NOT PART OF THE ...THE TRANSLATED SEQUENCES FOR CHAINS A AND B INCLUDE SIGNAL PEPTIDES WHICH ARE NOT PART OF THE ACTIVE, PROCESSED PROTEIN. THE SEQUENCES OF THE SIGNAL PEPTIDES ARE CHAIN A MLNNRRQILKSAGAAALGLGAGTLGWPGRHAFA CHAIN B MKRHNARTLAFSVVLGLSAAFAGSGLA R55

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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: 2.6 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.4
Details: 0.1M HEPES PH 7.4, 2.2M AMMONIUM SULFATE, 2% PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.074
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34463 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BLF

2blf


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.291 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1759 5.1 %RANDOM
Rwork0.161 ---
obs0.163 32619 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 79 354 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3952.0134981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37724.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63715536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5231518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4080.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.822326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.57133644
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.55721532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.83631335
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
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 97
Rwork0.191 2032

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