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- PDB-2blf: Sulfite dehydrogenase from Starkeya Novella -

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Basic information

Entry
Database: PDB / ID: 2blf
TitleSulfite dehydrogenase from Starkeya Novella
Components(Sulfite:cytochrome c oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / SULFITE OXIDASE / MOLYBDOPTERIN / C-TYPE CYTOCHROME / HEME / ELECTRON TRANSPORT
Function / homology
Function and homology information


sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / electron transfer 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 speciesStarkeya novella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBailey, S. / Kappler, U.
Citation
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.
#1: Journal: Acta Crystallogr. / Year: 2004
Title: Crystallisation and Preliminary X-Ray Analysis of Sulfite Dehydrogenase from Starkeya Novella.
Authors: Kappler, U. / Bailey, S.
History
DepositionMar 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Feb 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_ref / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _struct_conn.ptnr1_label_asym_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_type.id
Revision 2.2Nov 20, 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)50,2595
Polymers49,0402
Non-polymers1,2203
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.466, 92.513, 55.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE DIMER DESCRIBED HERE IS ACTUALLY A HETERO-DIMER, FORMEDFROM CHAINS A AND B. THE HETERO-DIMER IS KNOWN TO BE STABLE IN SOLUTION.

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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: 40194.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Starkeya novella (bacteria) / Gene: sorA / 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.) Starkeya novella (bacteria) / Gene: sorB / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA15

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Non-polymers , 4 types, 587 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.: 1 / 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.: 584 / Source method: isolated from a natural source / Formula: H2O

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Details

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

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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: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→17 Å / Num. obs: 259001 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / % possible all: 77.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SOX

1sox


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.67 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 2295 5.1 %RANDOM
Rwork0.136 ---
obs0.138 43048 95.3 %-
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: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 74 584 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223663
X-RAY DIFFRACTIONr_bond_other_d0.0010.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.342.0115019
X-RAY DIFFRACTIONr_angle_other_deg0.77537632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70824.156154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4811521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
X-RAY DIFFRACTIONr_nbd_refined0.2310.2685
X-RAY DIFFRACTIONr_nbd_other0.1890.23304
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21797
X-RAY DIFFRACTIONr_nbtor_other0.0830.22033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.44322897
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.88643664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.24341676
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.59461351
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.187 124
Rwork0.148 2359

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