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- PDB-2cb2: Sulfur Oxygenase Reductase from Acidianus Ambivalens -

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Basic information

Entry
Database: PDB / ID: 2cb2
TitleSulfur Oxygenase Reductase from Acidianus Ambivalens
ComponentsSULFUR OXYGENASE REDUCTASE
KeywordsOXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / MONONUCLEAR NON-HEME IRON / BIOGEOCHEMICAL SULFUR CYCLE / EXTREMOPHILE / THERMOPHILIC / ACIDOPHILIC / CYSTEINE PERSULPHIDE / ICOSATETRAMER / PROTO- ORGANELLE / NANO-STRUCTURE / COMPARTMENTALIZATION / 2-HIS-1- CARBOXYLATE FACIAL TRIAD / ARCHAEA / METAL-BINDING
Function / homologysulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase
Function and homology information
Biological speciesACIDIANUS AMBIVALENS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.7 Å
AuthorsUrich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C.
Citation
Journal: Science / Year: 2006
Title: X-Ray Structure of a Self-Compartmentalizing Sulfur Cycle Metalloenzyme
Authors: Urich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: The Sulfur Oxygenase Reductase from Acidianus Ambivalens is an Icosatetramer as Shown by Crystallization and Patterson Analysis
Authors: Urich, T. / Coelho, R. / Kletzin, A. / Frazao, C.
#2: Journal: J.Bacteriol. / Year: 1992
Title: Molecular Characterization of the Sor Gene, which Encodes the Sulfur Oxygenase-Reductase of the Thermoacidophilic Archaeum Desulfurolobus Ambivalens
Authors: Kletzin, A.
#3: Journal: J.Bacteriol. / Year: 1989
Title: Coupled Enzymatic Production of Sulfite, Thiosulfate, and Hydrogen Sulfide from Sulfur: Purification and Properties of a Sulfur Oxygenase Reductase from the Facultatively Anaerobic ...Title: Coupled Enzymatic Production of Sulfite, Thiosulfate, and Hydrogen Sulfide from Sulfur: Purification and Properties of a Sulfur Oxygenase Reductase from the Facultatively Anaerobic Archaebacterium Desulfurolobus Ambivalens
Authors: Kletzin, A.
History
DepositionDec 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 650 HELIX THE FOLLOWING HELIX DEFINITIONS HAVE BEEN PROVIDED BY THE DEPOSITOR AND ARE APPLICABLE TO ... HELIX THE FOLLOWING HELIX DEFINITIONS HAVE BEEN PROVIDED BY THE DEPOSITOR AND ARE APPLICABLE TO CHAINS A-F. 17-34, 83-92, 94-106, 133-142, 146-148, 173-187, 214-221,231-233, 239-241, 257-269, 271-281, 302-306
Remark 700 SHEET THE FOLLOWING SHEET BOUNDARIES HAVE BEEN PROVIDED BY THE DEPOSITOR AND ARE APPLICABLE TO ... SHEET THE FOLLOWING SHEET BOUNDARIES HAVE BEEN PROVIDED BY THE DEPOSITOR AND ARE APPLICABLE TO CHAINS A-F. 5-14 40-51, 71-80, 108-123, 160-168, 193-204, 246-250, 284-299

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFUR OXYGENASE REDUCTASE
B: SULFUR OXYGENASE REDUCTASE
C: SULFUR OXYGENASE REDUCTASE
D: SULFUR OXYGENASE REDUCTASE
E: SULFUR OXYGENASE REDUCTASE
F: SULFUR OXYGENASE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,89712
Polymers218,5626
Non-polymers3356
Water8,593477
1
A: SULFUR OXYGENASE REDUCTASE
B: SULFUR OXYGENASE REDUCTASE
C: SULFUR OXYGENASE REDUCTASE
D: SULFUR OXYGENASE REDUCTASE
E: SULFUR OXYGENASE REDUCTASE
F: SULFUR OXYGENASE REDUCTASE
hetero molecules

A: SULFUR OXYGENASE REDUCTASE
B: SULFUR OXYGENASE REDUCTASE
C: SULFUR OXYGENASE REDUCTASE
D: SULFUR OXYGENASE REDUCTASE
E: SULFUR OXYGENASE REDUCTASE
F: SULFUR OXYGENASE REDUCTASE
hetero molecules

A: SULFUR OXYGENASE REDUCTASE
B: SULFUR OXYGENASE REDUCTASE
C: SULFUR OXYGENASE REDUCTASE
D: SULFUR OXYGENASE REDUCTASE
E: SULFUR OXYGENASE REDUCTASE
F: SULFUR OXYGENASE REDUCTASE
hetero molecules

A: SULFUR OXYGENASE REDUCTASE
B: SULFUR OXYGENASE REDUCTASE
C: SULFUR OXYGENASE REDUCTASE
D: SULFUR OXYGENASE REDUCTASE
E: SULFUR OXYGENASE REDUCTASE
F: SULFUR OXYGENASE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,58948
Polymers874,24924
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)162.150, 162.150, 154.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 308
2116B1 - 308
3116C1 - 308
4116D1 - 308
5116E1 - 308
6116F1 - 308

NCS oper:
IDCodeMatrixVector
1given(-0.03667, -0.18329, 0.98237), (-0.18245, -0.96528, -0.18692), (0.98253, -0.18609, 0.00195)22.70297, 188.52853, 12.81951
2given(0.9659, -0.18227, -0.18387), (-0.18147, 0.02987, -0.98294), (0.18466, 0.98279, -0.00422)31.94385, 169.5654, -16.98899
3given(0.03532, 0.18611, 0.98189), (0.18187, 0.9649, -0.18943), (-0.98269, 0.18527, 0.00023)-12.92542, 2.67341, 142.23486
4given(-0.18433, 0.03404, 0.98227), (-0.9646, 0.18553, -0.18745), (-0.18862, -0.98205, -0.00136)7.15468, 158.73289, 172.33414
5given(0.92989, -0.3678, 0.00583), (-0.36779, -0.9299, -0.00325), (0.00662, 0.00088, -0.99998)35.30467, 186.32272, 154.73982

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Components

#1: Protein
SULFUR OXYGENASE REDUCTASE


Mass: 36427.031 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDIANUS AMBIVALENS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29082
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN PRESENCE OF OXYGEN IS ABLE TO SIMULTANEOUSLY OXIDATE AND REDUCE THE SULFUR ORIGINATING SULFITE, ...IN PRESENCE OF OXYGEN IS ABLE TO SIMULTANEOUSLY OXIDATE AND REDUCE THE SULFUR ORIGINATING SULFITE, SULFIDE AND THIOSULFATE AS PRODUCTS.

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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 growMethod: vapor diffusion, sitting drop / pH: 4.5
Details: VAPOUR DIFFUSION IN SITTING DROPS WITH 2MICRO-L OF PROTEIN SOLUTION, 13MG/L 50MM TRIS/HCL PH 7.5, AND 2MICRO-L OF WELL SOLUTION, 0.1 M SODIUM CITRATE PH 5.5 WITH 0.3 M MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.7→42.9 Å / Num. obs: 218799 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.5 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
ARP/wARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→111.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.114 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY ACTIVE ICOSATETRAMER IS OBTAINED BY APPLYING THE CRYSTALOGRAPHIC 4-FOLD ROTATION OPERATION TO THE ASYMMETRIC UNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1288 0.6 %THIN LAYERS
Rwork0.183 ---
obs0.183 217462 99.8 %-
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: 31.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14802 0 6 477 15285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02215484
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213897
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.94521006
X-RAY DIFFRACTIONr_angle_other_deg0.925332509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91451844
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_restr0.1160.22214
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216962
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023146
X-RAY DIFFRACTIONr_nbd_refined0.2150.22931
X-RAY DIFFRACTIONr_nbd_other0.2550.215539
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0970.28592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2497
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.2221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1431.59258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.047215094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40336226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3644.55912
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

Ens-ID: 1 / Number: 4613 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.285
2Bloose positional0.335
3Cloose positional0.315
4Dloose positional0.355
5Eloose positional0.375
6Floose positional0.35
1Aloose thermal1.210
2Bloose thermal1.0210
3Cloose thermal1.1610
4Dloose thermal1.0810
5Eloose thermal1.2510
6Floose thermal1.310
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 105
Rwork0.318 15766

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