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- PDB-3gyx: Crystal structure of adenylylsulfate reductase from Desulfovibrio... -

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Basic information

Entry
Database: PDB / ID: 3gyx
TitleCrystal structure of adenylylsulfate reductase from Desulfovibrio gigas
Components(Adenylylsulfate Reductase) x 2
KeywordsOXIDOREDUCTASE / Adenylylsulfate Reductase
Function / homology
Function and homology information


adenylyl-sulfate reductase / dissimilatory sulfate reduction / adenylyl-sulfate reductase activity / protein heterotetramerization / FAD binding / 4 iron, 4 sulfur cluster binding / protein heterodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain ...Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Alpha-Beta Plaits - #20 / Other non-globular / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Adenylylsulfate reductase subunit alpha / Adenylylsulfate reductase subunit beta
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChiang, Y.-L. / Hsieh, Y.-C. / Liu, E.-H. / Liu, M.-Y. / Chen, C.-J.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit
Authors: Chiang, Y.-L. / Hsieh, Y.-C. / Fang, J.-Y. / Liu, E.-H. / Huang, Y.-C. / Chuankhayan, P. / Jeyakanthan, J. / Liu, M.-Y. / Chan, S.I. / Chen, C.-J.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Adenylylsulfate Reductase
B: Adenylylsulfate Reductase
C: Adenylylsulfate Reductase
D: Adenylylsulfate Reductase
E: Adenylylsulfate Reductase
F: Adenylylsulfate Reductase
G: Adenylylsulfate Reductase
H: Adenylylsulfate Reductase
I: Adenylylsulfate Reductase
J: Adenylylsulfate Reductase
K: Adenylylsulfate Reductase
L: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,48430
Polymers557,55112
Non-polymers8,93318
Water1,24369
1
A: Adenylylsulfate Reductase
B: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-35 kcal/mol
Surface area31340 Å2
MethodPISA
2
C: Adenylylsulfate Reductase
D: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-36 kcal/mol
Surface area31330 Å2
MethodPISA
3
E: Adenylylsulfate Reductase
F: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-37 kcal/mol
Surface area31820 Å2
MethodPISA
4
G: Adenylylsulfate Reductase
H: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-36 kcal/mol
Surface area31200 Å2
MethodPISA
5
I: Adenylylsulfate Reductase
J: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-35 kcal/mol
Surface area31200 Å2
MethodPISA
6
K: Adenylylsulfate Reductase
L: Adenylylsulfate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4145
Polymers92,9252
Non-polymers1,4893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-32 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.629, 199.629, 317.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Adenylylsulfate Reductase


Mass: 74578.148 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: T2G6Z9*PLUS
#2: Protein
Adenylylsulfate Reductase


Mass: 18346.967 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: T2G899*PLUS
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.4
Details: 2M ammonium sulfate, 0.1M Tris, 1M guanidine hydrochloride, 0.2M sodium chloride, pH7.4, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 132767 / Num. obs: 122146 / % possible obs: 92 % / Observed criterion σ(I): 3.64 / Redundancy: 4.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.081 / Net I/σ(I): 13.63
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.64 / Num. unique all: 12375 / Rsym value: 0.446 / % possible all: 93.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JNR

1jnr


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.877 / SU B: 19.909 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24497 5561 5 %RANDOM
Rwork0.19226 ---
obs0.1949 105084 91.68 %-
all-112993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.365 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39054 0 414 69 39537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02240580
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.96854996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2354956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91323.7251836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.123156768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5815270
X-RAY DIFFRACTIONr_chiral_restr0.080.25724
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0230936
X-RAY DIFFRACTIONr_nbd_refined0.1860.220208
X-RAY DIFFRACTIONr_nbtor_refined0.3010.227466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21322
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.22
X-RAY DIFFRACTIONr_mcbond_it0.2241.525351
X-RAY DIFFRACTIONr_mcangle_it0.406239480
X-RAY DIFFRACTIONr_scbond_it0.394317981
X-RAY DIFFRACTIONr_scangle_it0.6234.515372
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 398 -
Rwork0.275 7755 -
obs--93.31 %

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