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- PDB-1jnz: Structure of adenylylsulfate reductase from the hyperthermophilic... -

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Basic information

Entry
Database: PDB / ID: 1jnz
TitleStructure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6 resolution
Components(adenylylsulfate ...) x 2
KeywordsOXIDOREDUCTASE / sulfur metabolism / adenylylsulfate reductase / iron-sulfur flavoprotein / catalysis
Function / homology
Function and homology information


succinate dehydrogenase activity / anaerobic respiration / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / plasma membrane
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 binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal 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 binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / 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 / 4Fe-4S binding domain / Other non-globular / 4Fe-4S dicluster domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / SULFITE ION / : / : / Adenylylsulfate reductase, subunit A (AprA) / Adenylylsulfate reductase, subunit B (AprB)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFritz, G. / Roth, A. / Schiffer, A. / Buechert, T. / Bourenkov, G. / Bartunik, H.D. / Huber, H. / Stetter, K.O. / Kroneck, P.M. / Ermler, U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution
Authors: Fritz, G. / Roth, A. / Schiffer, A. / Buchert, T. / Bourenkov, G. / Bartunik, H.D. / Huber, H. / Stetter, K.O. / Kroneck, P.M. / Ermler, U.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Archaeoglobus fulgidus
Authors: Roth, A. / Fritz, G. / Buechert, T. / Huber, H. / Stetter, K.O. / Ermler, U. / Kroneck, P.M.H.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,74212
Polymers180,6054
Non-polymers3,1388
Water28,3741575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28470 Å2
ΔGint-206 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.600, 113.500, 193.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe second part of the biological assembly is generated by rotation matrix -0.999932 -0.011239 0.003138 0.010826 -0.793178 0.608894 -0.004354 0.608886 0.793246 translation vector 174.4428 -1.5140 0.7045

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Components

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Adenylylsulfate ... , 2 types, 4 molecules ACBD

#1: Protein adenylylsulfate reductase


Mass: 73344.617 Da / Num. of mol.: 2 / Fragment: A SUBUNIT / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus DSM 4304 (archaea) / Species: Archaeoglobus fulgidus / Strain: DSM4304
References: GenBank: 2648886, UniProt: O28603*PLUS, adenylyl-sulfate reductase
#2: Protein adenylylsulfate reductase


Mass: 16957.650 Da / Num. of mol.: 2 / Fragment: B SUBUNIT / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus DSM 4304 (archaea) / Species: Archaeoglobus fulgidus / Strain: DSM4304
References: GenBank: 2648887, UniProt: O28604*PLUS, adenylyl-sulfate reductase

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Non-polymers , 4 types, 1583 molecules

#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1575 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, sodium acetate, sodium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 1999 / Details: Double focussing X-ray optics
RadiationMonochromator: double crystal monochromator, Si(111), 1st crystal water cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 54495 / Num. obs: 53527 / % possible obs: 79.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.5→2.53 Å / Rsym value: 0.26 / % possible all: 71.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JNR

1jnr


Resolution: 2.5→26.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2640335.29 / Data cutoff high rms absF: 2640335.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2705 5.1 %RANDOM
Rwork0.161 ---
obs0.161 53527 95.2 %-
all-54495 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0423 Å2 / ksol: 0.341563 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--3.33 Å20 Å2
3----3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12670 0 146 1575 14391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 433 5 %
Rwork0.144 8188 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COF.PAR
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4SULFIT_ADDUKT.PAR

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