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- PDB-5e7o: Crystal structure of the perchlorate reductase PcrAB mutant W461E... -

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Basic information

Entry
Database: PDB / ID: 5e7o
TitleCrystal structure of the perchlorate reductase PcrAB mutant W461E of PcrA from Azospira suillum PS
Components(DMSO reductase family type II enzyme, ...) x 2
KeywordsOXIDOREDUCTASE / oxidoreductase Mo-bisMGD Fe-S cluster perchlorate dissmilation
Function / homology
Function and homology information


oxidoreductase complex / anaerobic respiration / cellular respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / metal ion binding
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. / Molybdopterin oxidoreductase ...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
FE3-S4 CLUSTER / Chem-MD1 / Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / DMSO reductase family type II enzyme, iron-sulfur subunit / DMSO reductase family type II enzyme, molybdopterin subunit
Similarity search - Component
Biological speciesDechlorosoma suillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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.value / _pdbx_struct_oper_list.symmetry_operation / _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

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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
G: DMSO reductase family type II enzyme, molybdopterin subunit
H: DMSO reductase family type II enzyme, iron-sulfur subunit
I: DMSO reductase family type II enzyme, molybdopterin subunit
J: DMSO reductase family type II enzyme, iron-sulfur subunit
K: DMSO reductase family type II enzyme, molybdopterin subunit
L: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)856,14491
Polymers834,48312
Non-polymers21,66179
Water53,6492978
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)142,88718
Polymers139,0812
Non-polymers3,80616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-149 kcal/mol
Surface area37270 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)142,60814
Polymers139,0812
Non-polymers3,52812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-164 kcal/mol
Surface area37250 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)142,70015
Polymers139,0812
Non-polymers3,62013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-155 kcal/mol
Surface area37130 Å2
MethodPISA
4
G: DMSO reductase family type II enzyme, molybdopterin subunit
H: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,79417
Polymers139,0812
Non-polymers3,71415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint-144 kcal/mol
Surface area37360 Å2
MethodPISA
5
I: DMSO reductase family type II enzyme, molybdopterin subunit
J: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,54613
Polymers139,0812
Non-polymers3,46611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-157 kcal/mol
Surface area38170 Å2
MethodPISA
6
K: DMSO reductase family type II enzyme, molybdopterin subunit
L: DMSO reductase family type II enzyme, iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,60814
Polymers139,0812
Non-polymers3,52812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-162 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.588, 253.134, 135.797
Angle α, β, γ (deg.)90.00, 119.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DMSO reductase family type II enzyme, ... , 2 types, 12 molecules ACEGIKBDFHJL

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


Mass: 102012.758 Da / Num. of mol.: 6 / Fragment: UNP residues 29-927 / Mutation: W461E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS) (bacteria)
Strain: ATCC BAA-33 / DSM 13638 / PS / Gene: Dsui_0149 / Production host: Dechlorosoma suillum PS (bacteria) / References: UniProt: G8QM55
#2: Protein
DMSO reductase family type II enzyme, iron-sulfur subunit


Mass: 37067.809 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS) (bacteria)
Strain: ATCC BAA-33 / DSM 13638 / PS / Gene: Dsui_0148 / Production host: Dechlorosoma suillum PS (bacteria) / References: UniProt: G8QM54

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Non-polymers , 8 types, 3057 molecules

#3: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: Fe4S4
#4: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 6 / 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.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe3S4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2978 / 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: 2.42 Å3/Da / Density % sol: 49.26 % / Description: hexagonal plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 23% PEG3350, 0.1M Tris / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0062 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0062 Å / Relative weight: 1
Reflection twinOperator: l,k,-h-l / Fraction: 0.16
ReflectionResolution: 2.4→48.32 Å / Num. obs: 306131 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDD

4ydd


Resolution: 2.4→48.318 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2488 15564 5.08 %
Rwork0.1952 --
obs0.1976 306111 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58350 0 932 2978 62260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361189
X-RAY DIFFRACTIONf_angle_d0.65783258
X-RAY DIFFRACTIONf_dihedral_angle_d14.16136123
X-RAY DIFFRACTIONf_chiral_restr0.0458580
X-RAY DIFFRACTIONf_plane_restr0.00510674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44140.33756970.278714644X-RAY DIFFRACTION95
2.4414-2.48580.34498630.273514519X-RAY DIFFRACTION94
2.4858-2.53360.33977940.270314527X-RAY DIFFRACTION95
2.5336-2.58530.32486650.26314763X-RAY DIFFRACTION96
2.5853-2.64150.32087800.258114578X-RAY DIFFRACTION95
2.6415-2.70290.31087720.249114603X-RAY DIFFRACTION95
2.7029-2.77050.31217520.247814722X-RAY DIFFRACTION95
2.7705-2.84540.30366740.240214653X-RAY DIFFRACTION96
2.8454-2.9290.30087810.233714620X-RAY DIFFRACTION95
2.929-3.02350.31456760.231114771X-RAY DIFFRACTION96
3.0235-3.13150.30098090.221514471X-RAY DIFFRACTION95
3.1315-3.25680.2686660.210614738X-RAY DIFFRACTION95
3.2568-3.40490.28777520.202314592X-RAY DIFFRACTION95
3.4049-3.58420.24148010.187714444X-RAY DIFFRACTION94
3.5842-3.80850.2317480.182414379X-RAY DIFFRACTION94
3.8085-4.10210.21596750.166214442X-RAY DIFFRACTION93
4.1021-4.51410.2027330.151814261X-RAY DIFFRACTION92
4.5141-5.16530.19468170.149514258X-RAY DIFFRACTION92
5.1653-6.50040.20556420.169214572X-RAY DIFFRACTION94
6.5004-34.04440.17528380.143414527X-RAY DIFFRACTION93

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