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- PDB-5chc: Crystal structure of the perchlorate reductase PcrAB - substrate ... -

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Basic information

Entry
Database: PDB / ID: 5chc
TitleCrystal structure of the perchlorate reductase PcrAB - substrate analog SeO3 bound - from Azospira suillum PS
Components(DMSO reductase family type II enzyme, ...) x 2
KeywordsOXIDOREDUCTASE / electron-shuttling protein
Function / homology
Function and homology information


oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / electron transfer activity ...oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / electron transfer activity / metal ion binding / membrane
Similarity search - Function
DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. ...DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BISELENITE ION / FE3-S4 CLUSTER / Chem-MD1 / Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / SULFITE ION / DMSO reductase family type II enzyme, iron-sulfur subunit / DMSO reductase family type II enzyme, molybdopterin subunit
Similarity search - Component
Biological speciesAzospira oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsTsai, C.-L. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.
Authors: Youngblut, M.D. / Tsai, C.L. / Clark, I.C. / Carlson, H.K. / Maglaqui, A.P. / Gau-Pan, P.S. / Redford, S.A. / Wong, A. / Tainer, J.A. / Coates, J.D.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references / Other
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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
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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_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.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DMSO reductase family type II enzyme, molybdopterin subunit
B: DMSO reductase family type II enzyme, iron-sulfur subunit
C: DMSO reductase family type II enzyme, molybdopterin subunit
D: DMSO reductase family type II enzyme, iron-sulfur subunit
E: DMSO reductase family type II enzyme, molybdopterin subunit
F: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,83772
Polymers417,4136
Non-polymers12,42466
Water22,7171261
1
A: DMSO reductase family type II enzyme, molybdopterin subunit
B: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,69131
Polymers139,1382
Non-polymers4,55329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-198 kcal/mol
Surface area37530 Å2
MethodPISA
2
C: DMSO reductase family type II enzyme, molybdopterin subunit
D: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,04720
Polymers139,1382
Non-polymers3,90918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15070 Å2
ΔGint-218 kcal/mol
Surface area37400 Å2
MethodPISA
3
E: DMSO reductase family type II enzyme, molybdopterin subunit
F: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,10021
Polymers139,1382
Non-polymers3,96219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-228 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.926, 176.022, 193.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer confirmed by gel filtration and SAXS

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Components

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DMSO reductase family type II enzyme, ... , 2 types, 6 molecules ACEBDF

#1: Protein DMSO reductase family type II enzyme, molybdopterin subunit


Mass: 102069.859 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS) (bacteria)
Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM55
#2: Protein DMSO reductase family type II enzyme, iron-sulfur subunit


Mass: 37067.809 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS) (bacteria)
Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM54

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Non-polymers , 12 types, 1327 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mo
#5: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-MD1 / PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER


Mass: 740.557 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-BSY / BISELENITE ION


Mass: 127.966 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO3Se
#9: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO3
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1261 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.02 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG6K, 0.1 M Tris pH 8.5 / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.38→48.52 Å / Num. obs: 183135 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 13
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDD

4ydd


Resolution: 2.38→48.52 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 9139 4.99 %
Rwork0.1704 --
obs0.1732 183004 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29138 0 539 1261 30938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0130568
X-RAY DIFFRACTIONf_angle_d1.3841570
X-RAY DIFFRACTIONf_dihedral_angle_d15.9811231
X-RAY DIFFRACTIONf_chiral_restr0.0524277
X-RAY DIFFRACTIONf_plane_restr0.0075322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4070.31213100.24635695X-RAY DIFFRACTION100
2.407-2.43540.31913090.2535759X-RAY DIFFRACTION100
2.4354-2.46510.3442830.24495742X-RAY DIFFRACTION100
2.4651-2.49630.2713080.22725720X-RAY DIFFRACTION100
2.4963-2.52910.30973100.23885742X-RAY DIFFRACTION100
2.5291-2.56380.31123150.22935771X-RAY DIFFRACTION100
2.5638-2.60040.31142960.22495707X-RAY DIFFRACTION100
2.6004-2.63920.30322640.22485783X-RAY DIFFRACTION100
2.6392-2.68040.28753130.20945739X-RAY DIFFRACTION100
2.6804-2.72440.28412930.20745783X-RAY DIFFRACTION100
2.7244-2.77130.29183250.20965766X-RAY DIFFRACTION100
2.7713-2.82170.26663140.2025706X-RAY DIFFRACTION100
2.8217-2.8760.27723040.20135781X-RAY DIFFRACTION100
2.876-2.93470.2763130.20055758X-RAY DIFFRACTION100
2.9347-2.99850.26623130.20085740X-RAY DIFFRACTION100
2.9985-3.06820.26412780.20465796X-RAY DIFFRACTION100
3.0682-3.1450.26232840.19425786X-RAY DIFFRACTION100
3.145-3.230.26363050.1975793X-RAY DIFFRACTION100
3.23-3.3250.23613020.18825760X-RAY DIFFRACTION100
3.325-3.43230.24163220.18715769X-RAY DIFFRACTION100
3.4323-3.55490.23952730.18085824X-RAY DIFFRACTION100
3.5549-3.69720.24172800.1775829X-RAY DIFFRACTION100
3.6972-3.86540.21882760.15825859X-RAY DIFFRACTION100
3.8654-4.06910.20653000.1495812X-RAY DIFFRACTION100
4.0691-4.32390.17773440.13425799X-RAY DIFFRACTION100
4.3239-4.65750.16643240.12655827X-RAY DIFFRACTION100
4.6575-5.12580.16113130.12025859X-RAY DIFFRACTION100
5.1258-5.86640.18263140.1265894X-RAY DIFFRACTION100
5.8664-7.38680.18233010.12755945X-RAY DIFFRACTION100
7.3868-48.53150.14943530.11826121X-RAY DIFFRACTION100

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