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- PDB-2c1d: Crystal structure of SoxXA from P. pantotrophus -

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Basic information

Entry
Database: PDB / ID: 2c1d
TitleCrystal structure of SoxXA from P. pantotrophus
Components
  • SOXA
  • SOXX
KeywordsOXIDOREDUCTASE / SULFUR OXIDATION / CYTOCHROME-C-TYPE
Function / homology
Function and homology information


L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate-cyanide sulfurtransferase activity / periplasmic space / electron transfer activity / oxidoreductase activity / iron ion binding ...L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate-cyanide sulfurtransferase activity / periplasmic space / electron transfer activity / oxidoreductase activity / iron ion binding / protein heterodimerization activity / heme binding / zinc ion binding / metal ion binding
Similarity search - Function
L-cysteine S-thiosulfotransferase subunit SoxA / Sulfur oxidation c-type cytochrome SoxX / SoxA/TsdA, cytochrome c domain / Multiheme cytochrome c family profile. / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...L-cysteine S-thiosulfotransferase subunit SoxA / Sulfur oxidation c-type cytochrome SoxX / SoxA/TsdA, cytochrome c domain / Multiheme cytochrome c family profile. / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / L-cysteine S-thiosulfotransferase subunit SoxA / SoxX protein
Similarity search - Component
Biological speciesPARACOCCUS DENITRIFICANS (bacteria)
PARACOCCUS PANTOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDambe, T. / Quentmeier, A. / Rother, D. / Friedrich, C. / Scheidig, A.J.
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Structure of the Cytochrome Complex Soxxa of Paracoccus Pantotrophus, a Heme Enzyme Initiating Chemotrophic Sulfur Oxidation.
Authors: Dambe, T. / Quentmeier, A. / Rother, D. / Friedrich, C. / Scheidig, A.J.
History
DepositionSep 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOXA
B: SOXX
C: SOXA
D: SOXX
E: SOXA
F: SOXX
G: SOXA
H: SOXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,65532
Polymers174,4488
Non-polymers8,20724
Water38,7502151
1
A: SOXA
B: SOXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7299
Polymers43,6122
Non-polymers2,1177
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SOXA
D: SOXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6648
Polymers43,6122
Non-polymers2,0526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: SOXA
F: SOXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5987
Polymers43,6122
Non-polymers1,9865
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: SOXA
H: SOXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6648
Polymers43,6122
Non-polymers2,0526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.860, 180.010, 117.930
Angle α, β, γ (deg.)90.00, 92.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SOXA


Mass: 29281.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DIHEME CYTOCHROME C / Source: (gene. exp.) PARACOCCUS DENITRIFICANS (bacteria) / Production host: PARACOCCUS PANTOTROPHUS (bacteria) / References: UniProt: O33434
#2: Protein
SOXX


Mass: 14330.198 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CYTOCHROME C / Source: (gene. exp.) PARACOCCUS PANTOTROPHUS (bacteria) / Production host: PARACOCCUS PANTOTROPHUS (bacteria) / References: UniProt: Q9LCV0
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCRYSTAL STRUCTURE CHAINS A TO H DO NOT CONTAIN LEADER PEPTIDE

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.737
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.737 Å / Relative weight: 1
ReflectionResolution: 1.9→19.5 Å / Num. obs: 631082 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.9 / % possible all: 62.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H33

1h33


Resolution: 1.92→119.52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.361 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 6346 5 %RANDOM
Rwork0.159 ---
obs0.161 120519 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.13 Å2
2---1.52 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.92→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12199 0 528 2151 14878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02113056
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211412
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.07317868
X-RAY DIFFRACTIONr_angle_other_deg0.885326488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34851596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.21832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214756
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022488
X-RAY DIFFRACTIONr_nbd_refined0.2730.23227
X-RAY DIFFRACTIONr_nbd_other0.2480.214204
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.26669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.21488
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.2113
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.2209
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.2127
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.57944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.278212720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22135112
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5474.55148
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: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 355
Rwork0.258 6632

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