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- PDB-6cz9: The arsenate respiratory reductase (Arr) complex from Shewanella ... -

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Basic information

Entry
Database: PDB / ID: 6cz9
TitleThe arsenate respiratory reductase (Arr) complex from Shewanella sp. ANA-3 bound to arsenite
Components
  • 4Fe-4S ferredoxin, iron-sulfur binding domain protein
  • ArrA
KeywordsOXIDOREDUCTASE / arsenate / molybdoprotein / molybdopterin / arsenite
Function / homology
Function and homology information


arsenate reductase (donor) / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / metal ion binding
Similarity search - Function
Tetrathionate reductase subunit A, MopB domain / : / : / : / 4Fe-4S binding domain / ADC-like domains / : / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain ...Tetrathionate reductase subunit A, MopB domain / : / : / : / 4Fe-4S binding domain / ADC-like domains / : / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / N-terminal domain of TfIIb / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ARSENITE / FORMIC ACID / Chem-MGD / MOLYBDENUM ATOM / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / IRON/SULFUR CLUSTER / Arsenate respiratory reductase iron-sulfur subunit ArrB / Arsenate respiratory reductase molybdopterin-containing subunit ArrA
Similarity search - Component
Biological speciesShewanella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsGlasser, N.R. / Newman, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL117328-03 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations.
Authors: Glasser, N.R. / Oyala, P.H. / Osborne, T.H. / Santini, J.M. / Newman, D.K.
History
DepositionApr 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 3, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ArrA
B: 4Fe-4S ferredoxin, iron-sulfur binding domain protein
C: ArrA
D: 4Fe-4S ferredoxin, iron-sulfur binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,57333
Polymers233,8264
Non-polymers7,74729
Water41,1822286
1
A: ArrA
B: 4Fe-4S ferredoxin, iron-sulfur binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,78017
Polymers116,9132
Non-polymers3,86715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-167 kcal/mol
Surface area32110 Å2
MethodPISA
2
C: ArrA
D: 4Fe-4S ferredoxin, iron-sulfur binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,79416
Polymers116,9132
Non-polymers3,88114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-170 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.512, 86.306, 147.367
Angle α, β, γ (deg.)90.00, 127.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein ArrA / Molybdopterin oxidoreductase


Mass: 91143.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. (strain ANA-3) (bacteria)
Strain: ANA-3 / Gene: arrA, Shewana3_2341 / Production host: Shewanella sp. ANA-3 (bacteria) / References: UniProt: Q7WTU0
#2: Protein 4Fe-4S ferredoxin, iron-sulfur binding domain protein / ArrB


Mass: 25769.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. (strain ANA-3) (bacteria)
Strain: ANA-3 / Gene: arrB, Shewana3_2340 / Production host: Shewanella sp. ANA-3 (bacteria) / References: UniProt: Q7WTT9

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Non-polymers , 8 types, 2315 molecules

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


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4
#4: 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.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-AST / ARSENITE


Mass: 122.920 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AsO3
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2286 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 10 mg/ml protein, 15% PEG 2000 MME, 150 mM KSCN, 50 mM HEPES (adjusted to pH 7.5 with NaOH), microseeded; cryoprotected in 30% PEG 2000 MME, 100 mM KSCN, 1 M sodium formate, 50 mM HEPES (pH ...Details: 10 mg/ml protein, 15% PEG 2000 MME, 150 mM KSCN, 50 mM HEPES (adjusted to pH 7.5 with NaOH), microseeded; cryoprotected in 30% PEG 2000 MME, 100 mM KSCN, 1 M sodium formate, 50 mM HEPES (pH 7.5), 5 mM sodium arsenite

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.37 Å / Num. obs: 209823 / % possible obs: 98.35 % / Redundancy: 6.9 % / Rpim(I) all: 0.032 / Net I/σ(I): 17.49
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.27 / Num. unique obs: 20962 / Rpim(I) all: 0.313 / % possible all: 98.89

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.8→39.369 Å / SU ML: 0.16 / σ(F): 1.92 / Phase error: 17.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1694 5129 1.25 %
Rwork0.1422 --
obs0.1426 411525 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16227 0 333 2286 18846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517140
X-RAY DIFFRACTIONf_angle_d0.9923380
X-RAY DIFFRACTIONf_dihedral_angle_d15.3926176
X-RAY DIFFRACTIONf_chiral_restr0.0552490
X-RAY DIFFRACTIONf_plane_restr0.0052983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.27051910.250913589X-RAY DIFFRACTION99
1.8205-1.84190.21951660.232913734X-RAY DIFFRACTION99
1.8419-1.86430.23811660.225413529X-RAY DIFFRACTION99
1.8643-1.88790.23761850.218613691X-RAY DIFFRACTION98
1.8879-1.91280.21161700.213113597X-RAY DIFFRACTION98
1.9128-1.9390.21911650.206813528X-RAY DIFFRACTION98
1.939-1.96670.21111680.202513536X-RAY DIFFRACTION98
1.9667-1.9960.20281470.189413582X-RAY DIFFRACTION98
1.996-2.02720.24041700.191813449X-RAY DIFFRACTION98
2.0272-2.06050.22471840.183313498X-RAY DIFFRACTION97
2.0605-2.0960.21591690.179513207X-RAY DIFFRACTION95
2.096-2.13410.16481540.16813416X-RAY DIFFRACTION97
2.1341-2.17510.20661790.156913711X-RAY DIFFRACTION99
2.1751-2.21950.18231750.152613602X-RAY DIFFRACTION99
2.2195-2.26780.16591800.146113664X-RAY DIFFRACTION99
2.2678-2.32050.19371590.141113545X-RAY DIFFRACTION99
2.3205-2.37860.15881830.138113613X-RAY DIFFRACTION98
2.3786-2.44290.15881670.136213568X-RAY DIFFRACTION98
2.4429-2.51470.18111640.135713533X-RAY DIFFRACTION98
2.5147-2.59590.19121810.137613561X-RAY DIFFRACTION98
2.5959-2.68860.18081590.140413164X-RAY DIFFRACTION95
2.6886-2.79630.20191590.138513567X-RAY DIFFRACTION98
2.7963-2.92350.15171810.141613652X-RAY DIFFRACTION99
2.9235-3.07760.15881730.146513767X-RAY DIFFRACTION99
3.0776-3.27030.2231760.14713621X-RAY DIFFRACTION98
3.2703-3.52270.15161600.135813490X-RAY DIFFRACTION98
3.5227-3.87690.16551710.119913254X-RAY DIFFRACTION96
3.8769-4.43720.11391710.100213486X-RAY DIFFRACTION98
4.4372-5.58790.10181770.099713746X-RAY DIFFRACTION99
5.5879-39.37830.15671790.133913496X-RAY DIFFRACTION98

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