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- PDB-3bxv: Crystal structure studies on sulfur oxygenase reductase from Acid... -

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Basic information

Entry
Database: PDB / ID: 3bxv
TitleCrystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis
ComponentsSulfur oxygenase/reductase
KeywordsOXIDOREDUCTASE / beta barrel
Function / homologySulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesAcidianus tengchongenses (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChang, W.R. / Li, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis
Authors: Li, M. / Chen, Z. / Zhang, P. / Pan, X. / Jiang, C. / An, X. / Liu, S. / Chang, W.
History
DepositionJan 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Apr 30, 2025Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfur oxygenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2392
Polymers35,1831
Non-polymers561
Water95553
1
A: Sulfur oxygenase/reductase
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)845,74348
Polymers844,40324
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area137710 Å2
ΔGint-1171 kcal/mol
Surface area213110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.130, 159.130, 159.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Sulfur oxygenase/reductase


Mass: 35183.457 Da / Num. of mol.: 1 / Mutation: K174E, V238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus tengchongenses (archaea) / Plasmid: pBV220 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q977W3, sulfur oxygenase/reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer detailsWE ARE NOT SURE IF THIS ION IS FERRIC OR FERROUS, AND WE PUT IT AS FE(III) IN THIS ENTRY.

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.08M NaCitr3, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 9761 / Num. obs: 9761 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 22.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.8 / Num. unique all: 905 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2CB2

2cb2


Resolution: 2.7→29.05 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 975 -random
Rwork0.192 ---
all0.194 9761 --
obs0.194 9417 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 1 53 2529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.73

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