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- PDB-6qmv: E87D sulfur oxygenase reductase -

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Basic information

Entry
Database: PDB / ID: 6qmv
TitleE87D sulfur oxygenase reductase
ComponentsSulfur oxygenase/reductase
KeywordsOXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / 2-HIS-1-CARBOXYLATE FACIAL TRIAD / CYSTEINE PERSULPHURATION / BIOGEOCHEMICAL SULFUR CYCLE
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 / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsFrazao, C. / Klezin, A. / Veith, A.
Funding support Germany, Portugal, 2items
OrganizationGrant numberCountry
German Research FoundationKl885-6/1 Germany
Fundacao para a Ciencia e a TecnologiaLIOA-01-0145-FEDER-007660 Portugal
Citation
Journal: To Be Published
Title: Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels
Authors: Frazao, C. / Klezin, A.
#1: 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.
#2: Journal: Front Microbiol / Year: 2011
Title: Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens.
Authors: Veith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)218,7796
Polymers218,7796
Non-polymers00
Water26,5361473
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

A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase

A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase

A: Sulfur oxygenase/reductase
B: Sulfur oxygenase/reductase
C: Sulfur oxygenase/reductase
D: Sulfur oxygenase/reductase
E: Sulfur oxygenase/reductase
F: Sulfur oxygenase/reductase


Theoretical massNumber of molelcules
Total (without water)875,11524
Polymers875,11524
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area133050 Å2
ΔGint-839 kcal/mol
Surface area209450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.920, 161.920, 154.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Sulfur oxygenase/reductase / Sulfur oxygenase reductase / SOR


Mass: 36463.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: the crystal structure shows some cys residues chemically modified, namely css_31 and tsy_104
Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1473 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 305 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M ADA pH 6, 3-5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.87→45.97 Å / Num. obs: 163003 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.0416 / Rrim(I) all: 0.09 / Rsym value: 0.078 / Net I/σ(I): 14.78
Reflection shellResolution: 1.87→1.98 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 25653 / Rpim(I) all: 0.225 / Rrim(I) all: 0.577 / Rsym value: 0.497 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CB2

2cb2


Resolution: 1.87→43.118 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.1926 1985 1.22 %
Rwork0.1593 --
obs0.1597 162955 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→43.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14808 0 0 1473 16281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715444
X-RAY DIFFRACTIONf_angle_d0.90620947
X-RAY DIFFRACTIONf_dihedral_angle_d12.0399283
X-RAY DIFFRACTIONf_chiral_restr0.0572217
X-RAY DIFFRACTIONf_plane_restr0.0062679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8659-1.91260.32191330.26210688X-RAY DIFFRACTION93
1.9126-1.96430.26741330.21811531X-RAY DIFFRACTION100
1.9643-2.02210.23531460.187611589X-RAY DIFFRACTION100
2.0221-2.08740.25491430.192611542X-RAY DIFFRACTION100
2.0874-2.1620.2821420.237811169X-RAY DIFFRACTION96
2.162-2.24850.2211350.18511573X-RAY DIFFRACTION100
2.2485-2.35090.20331520.164111537X-RAY DIFFRACTION100
2.3509-2.47480.20321320.158811605X-RAY DIFFRACTION100
2.4748-2.62980.17831490.151611575X-RAY DIFFRACTION100
2.6298-2.83280.22061410.152111620X-RAY DIFFRACTION100
2.8328-3.11780.17981440.151811572X-RAY DIFFRACTION100
3.1178-3.56880.17581470.141511600X-RAY DIFFRACTION100
3.5688-4.49560.14691430.126911642X-RAY DIFFRACTION100
4.4956-43.12980.15381450.142211727X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 45.7717 Å / Origin y: 100.4598 Å / Origin z: 77.3231 Å
111213212223313233
T0.1133 Å20.0143 Å20.0058 Å2-0.1218 Å20.0118 Å2--0.1278 Å2
L0.0363 °20.0038 °2-0.0068 °2-0.0298 °20.0136 °2--0.071 °2
S0.0087 Å °-0.0002 Å °0.0112 Å °0.0032 Å °0.0031 Å °0.0188 Å °-0.0058 Å °-0.0302 Å °-0.0116 Å °
Refinement TLS groupSelection details: ALL

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