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- PDB-5ch7: Crystal structure of the perchlorate reductase PcrAB - Phe164 gat... -

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Basic information

Entry
Database: PDB / ID: 5ch7
TitleCrystal structure of the perchlorate reductase PcrAB - Phe164 gate switch intermediate - 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 / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / oxidoreductase activity ...oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / oxidoreductase 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
ACETATE 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: 2.2 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
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 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_value_order / _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_conn.ptnr2_label_seq_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)429,08460
Polymers417,4136
Non-polymers11,67154
Water35,5981976
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)143,19222
Polymers139,1382
Non-polymers4,05520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-192 kcal/mol
Surface area37190 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)142,97319
Polymers139,1382
Non-polymers3,83517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-210 kcal/mol
Surface area36750 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)142,91919
Polymers139,1382
Non-polymers3,78117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-218 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.884, 175.667, 193.278
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, 2030 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.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO3
#12: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1976 / 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: 2.7 Å3/Da / Density % sol: 54.48 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 20% PEG6K, 0.1 M Tris pH 8.5 anaerobically / PH range: 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: 2.2→48.38 Å / Num. obs: 228466 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PcrAB_4YDD

Resolution: 2.2→48.38 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 11302 4.95 %
Rwork0.178 --
obs0.1807 228334 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29116 0 503 1976 31595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01130576
X-RAY DIFFRACTIONf_angle_d1.46641604
X-RAY DIFFRACTIONf_dihedral_angle_d15.86911246
X-RAY DIFFRACTIONf_chiral_restr0.0584275
X-RAY DIFFRACTIONf_plane_restr0.0075331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.31713570.26147176X-RAY DIFFRACTION100
2.225-2.25120.33033790.26937181X-RAY DIFFRACTION100
2.2512-2.27860.29393940.25497105X-RAY DIFFRACTION100
2.2786-2.30750.29943810.2437156X-RAY DIFFRACTION100
2.3075-2.33780.30863820.24657111X-RAY DIFFRACTION100
2.3378-2.36990.30213970.24057211X-RAY DIFFRACTION100
2.3699-2.40370.30423560.23527155X-RAY DIFFRACTION100
2.4037-2.43960.28283250.23417235X-RAY DIFFRACTION100
2.4396-2.47770.29283680.23137171X-RAY DIFFRACTION100
2.4777-2.51830.31083630.22117203X-RAY DIFFRACTION100
2.5183-2.56180.30073860.22357169X-RAY DIFFRACTION100
2.5618-2.60830.29393830.22247211X-RAY DIFFRACTION100
2.6083-2.65850.26174110.20567159X-RAY DIFFRACTION100
2.6585-2.71280.2774090.21037151X-RAY DIFFRACTION100
2.7128-2.77170.27623580.20737197X-RAY DIFFRACTION100
2.7717-2.83620.26373790.20437227X-RAY DIFFRACTION100
2.8362-2.90710.26113640.19967178X-RAY DIFFRACTION100
2.9071-2.98570.27093590.20527271X-RAY DIFFRACTION100
2.9857-3.07360.26043640.20017239X-RAY DIFFRACTION100
3.0736-3.17280.27473570.19627228X-RAY DIFFRACTION100
3.1728-3.28610.26783570.19757265X-RAY DIFFRACTION100
3.2861-3.41770.25433870.19097221X-RAY DIFFRACTION100
3.4177-3.57320.22844200.17867230X-RAY DIFFRACTION100
3.5732-3.76150.21943880.1687233X-RAY DIFFRACTION100
3.7615-3.9970.20183790.14737289X-RAY DIFFRACTION100
3.997-4.30550.16843520.13267332X-RAY DIFFRACTION100
4.3055-4.73840.17363900.12467307X-RAY DIFFRACTION100
4.7384-5.42330.17183730.12187347X-RAY DIFFRACTION100
5.4233-6.82970.16783830.12987418X-RAY DIFFRACTION100
6.8297-48.39510.16274010.12547656X-RAY DIFFRACTION100

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