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- PDB-2a5w: Crystal structure of the oxidized gamma-subunit of the dissimilat... -

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Basic information

Entry
Database: PDB / ID: 2a5w
TitleCrystal structure of the oxidized gamma-subunit of the dissimilatory sulfite reductase (DsrC) from Archaeoglobus fulgidus
Componentssulfite reductase, desulfoviridin-type subunit gamma (dsvC)
KeywordsOXIDOREDUCTASE / orthogonal helix bundle
Function / homology
Function and homology information


sulfur carrier activity / tRNA wobble position uridine thiolation / 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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich ...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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sulfite reductase, desulfoviridin-type subunit gamma (DsvC)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMander, G.J. / Weiss, M.S. / Hedderich, R. / Kahnt, J. / Ermler, U. / Warkentin, E.
CitationJournal: Febs Lett. / Year: 2005
Title: X-ray structure of the gamma-subunit of a dissimilatory sulfite reductase: Fixed and flexible C-terminal arms.
Authors: Mander, G.J. / Weiss, M.S. / Hedderich, R. / Kahnt, J. / Ermler, U. / Warkentin, E.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
B: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
C: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8807
Polymers40,4963
Non-polymers3844
Water3,351186
1
A: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6913
Polymers13,4991
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6913
Polymers13,4991
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)


Theoretical massNumber of molelcules
Total (without water)13,4991
Polymers13,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
C: sulfite reductase, desulfoviridin-type subunit gamma (dsvC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1894
Polymers26,9972
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-41 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.22, 64.80, 129.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sulfite reductase, desulfoviridin-type subunit gamma (dsvC)


Mass: 13498.659 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: DsrC / Plasmid: pCR2.1-TOPO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28055
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.9 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000, Mes/KOH, (NH4)2 SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 24295 / Num. obs: 24295 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.066 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 2005 / Rsym value: 0.38 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SAU

1sau


Resolution: 2.1→28.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.877 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.18 / Stereochemistry target values: Engh & Huber
Details: The authors state that the SSBOND between CYS 77 and CYS 85 is partially split, i.e., in only about 50% of all the instances there is a bond and none for the remainder.
RfactorNum. reflection% reflectionSelection details
Rfree0.23062 1165 4.8 %RANDOM
Rwork0.20223 ---
all0.2036 23085 --
obs0.20363 23085 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--1.53 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 20 186 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222925
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9913962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26723.913138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1115530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022211
X-RAY DIFFRACTIONr_nbd_refined0.1970.21369
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.216
X-RAY DIFFRACTIONr_mcbond_it0.7351.51803
X-RAY DIFFRACTIONr_mcangle_it1.11422799
X-RAY DIFFRACTIONr_scbond_it1.78731328
X-RAY DIFFRACTIONr_scangle_it2.8334.51163
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 72 -
Rwork0.202 1303 -
obs-1303 76.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.29340.63710.34061.63550.64342.14590.05050.1158-0.0990.06620.0664-0.22480.12170.0012-0.1169-0.07840.0128-0.0307-0.0328-0.0342-0.012466.0905-10.494742.7372
21.89230.40320.11071.9536-0.2131.23620.10820.1286-0.02930.01630.0006-0.0204-0.0491-0.0584-0.1088-0.07860.00810.0235-0.02450.0147-0.04747.84378.925147.456
33.2847-1.1041-0.66982.5798-0.33222.89790.28910.10480.2604-0.5498-0.1366-0.07260.0944-0.2363-0.15250.06310.07040.0443-0.09070.0424-0.110839.09432.983157.0129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1152 - 115
2X-RAY DIFFRACTION2BB2 - 1152 - 115
3X-RAY DIFFRACTION3CC2 - 1152 - 115

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