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- PDB-2xsj: Structure of desulforubidin from Desulfomicrobium norvegicum -

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Basic information

Entry
Database: PDB / ID: 2xsj
TitleStructure of desulforubidin from Desulfomicrobium norvegicum
Components
  • (SULFITE REDUCTASE ...) x 2
  • SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY
KeywordsOXIDOREDUCTASE / DISSIMILATORY SULFITE REDUCTASE / SULFUR METABOLISM / DSRABC
Function / homology
Function and homology information


dissimilatory sulfite reductase activity / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / heme binding / metal ion binding / cytoplasm
Similarity search - Function
DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Alpha-Beta Plaits - #2500 / Alpha-Beta Plaits - #3340 ...DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Alpha-Beta Plaits - #2500 / Alpha-Beta Plaits - #3340 / Helix Hairpins - #1420 / Sulphite reductase, dissimilatory-type alpha subunit / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Alpha-Beta Plaits - #20 / Helix Hairpins / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / SULFITE ION / SIROHEME / Sulfur relay protein, TusE/DsrC/DsvC family / Sulfite reductase beta subunit / Sulfite reductase alpha subunit
Similarity search - Component
Biological speciesDESULFOMICROBIUM NORVEGICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOliveira, T.F. / Khan, A.R. / Pereira, I.A.C. / Archer, M.
CitationJournal: Front.Microbiol. / Year: 2011
Title: Structural Insights Into Dissimilatory Sulfite Reductases: Structure of Desulforubidin from Desulfomicrobium Norvegicum
Authors: Oliveira, T.F. / Franklin, E. / Afonso, J.P. / Khan, A.R. / Oldham, N.J. / Pereira, I.A.C. / Archer, M.
History
DepositionSep 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 2.0Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFITE REDUCTASE ALPHA SUBUNIT
B: SULFITE REDUCTASE BETA SUBUNIT
C: SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY
D: SULFITE REDUCTASE ALPHA SUBUNIT
E: SULFITE REDUCTASE BETA SUBUNIT
F: SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,82720
Polymers209,1876
Non-polymers6,64014
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55250 Å2
ΔGint-478.9 kcal/mol
Surface area57420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.340, 135.090, 178.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 5

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA2 - 4372 - 437
21ARGARGDD2 - 4372 - 437
12PHEPHEBB2 - 3862 - 386
22PHEPHEEE2 - 3862 - 386
13VALVALCC2 - 1052 - 105
23VALVALFF2 - 1052 - 105

NCS ensembles :
ID
1
2
3

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Components

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SULFITE REDUCTASE ... , 2 types, 4 molecules ADBE

#1: Protein SULFITE REDUCTASE ALPHA SUBUNIT


Mass: 49398.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOMICROBIUM NORVEGICUM (bacteria) / References: UniProt: Q93UT1, EC: 1.8.99.3
#2: Protein SULFITE REDUCTASE BETA SUBUNIT


Mass: 43335.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: COVALENT BOND BETWEEN THE SG OF CYS 104C/E AND THE 20- MESO CARBON OF THE CATALYTIC SIROHEME PORPHYRIN RING
Source: (natural) DESULFOMICROBIUM NORVEGICUM (bacteria) / References: UniProt: Q93UT0, EC: 1.8.99.3

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Protein , 1 types, 2 molecules CF

#3: Protein SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY


Mass: 11858.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOMICROBIUM NORVEGICUM (bacteria) / References: UniProt: C7LV29*PLUS, EC: 1.8.99.3

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Non-polymers , 4 types, 1055 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#6: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 2.7 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5
Details: 20% PEG 3350, 0.1 M BISTRIS PROPANE PH 7.5 AND 0.2 M K/NA TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.53→45.1 Å / Num. obs: 79925 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V4J

2v4j


Resolution: 2.5→44.51 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.544 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20848 4114 5 %RANDOM
Rwork0.15622 ---
obs0.1588 78140 98.58 %-
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: 18.344 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---0.8 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14614 0 324 1041 15979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.97920940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4651844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45824.011708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.777152532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421592
X-RAY DIFFRACTIONr_chiral_restr0.1020.22163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111882
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6171.59181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23214772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.15336234
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4534.56072
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1744medium positional0.060.5
12D1744medium positional0.060.5
21B1536medium positional0.060.5
22E1536medium positional0.060.5
31C416medium positional0.10.5
32F416medium positional0.10.5
11A1712loose positional0.215
12D1712loose positional0.215
21B1486loose positional0.25
22E1486loose positional0.25
31C409loose positional0.465
32F409loose positional0.465
11A1744medium thermal0.652
12D1744medium thermal0.652
21B1536medium thermal0.712
22E1536medium thermal0.712
31C416medium thermal1.472
32F416medium thermal1.472
11A1712loose thermal1.0710
12D1712loose thermal1.0710
21B1486loose thermal1.0510
22E1486loose thermal1.0510
31C409loose thermal1.8210
32F409loose thermal1.8210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 231 -
Rwork0.187 5005 -
obs--86.77 %

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