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- PDB-4ywo: Mercuric reductase from Metallosphaera sedula -

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Basic information

Entry
Database: PDB / ID: 4ywo
TitleMercuric reductase from Metallosphaera sedula
ComponentsMercuric reductase
KeywordsOXIDOREDUCTASE / mercuric reductase / FAD
Function / homology
Function and homology information


mercury(II) reductase / mercury (II) reductase (NADP+) activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / detoxification of mercury ion / mercury ion binding / NAD(P)H dehydrogenase (quinone) activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Mercury(II) reductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase ...Mercury(II) reductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Mercuric reductase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsArtz, J.H. / Zadvornyy, O.A. / White, S. / Peters, J.W.
CitationJournal: Front Bioeng Biotechnol / Year: 2015
Title: Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula.
Authors: Artz, J.H. / White, S.N. / Zadvornyy, O.A. / Fugate, C.J. / Hicks, D. / Gauss, G.H. / Posewitz, M.C. / Boyd, E.S. / Peters, J.W.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3077
Polymers50,0601
Non-polymers1,2466
Water3,819212
1
A: Mercuric reductase
hetero molecules

A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,61314
Polymers100,1212
Non-polymers2,49212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area11530 Å2
ΔGint-65 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.679, 95.895, 104.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Mercuric reductase


Mass: 50060.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (strain ATCC 51363 / DSM 5348) (archaea)
Strain: ATCC 51363 / DSM 5348 / Gene: Msed_1241 / Production host: Escherichia coli (E. coli) / References: UniProt: A4YG49
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.085 M TRIS, 15% v/v glycerol, 14% w/v PEG400, 0.19 M LiSO4, and 20 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.62→70.65 Å / Num. obs: 71541 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.1687 / Rsym value: 0.1957 / Net I/σ(I): 13.2
Reflection shellResolution: 1.62→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Blu-Icedata collection
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZK7

1zk7


Resolution: 1.62→70.65 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.522 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3604 5 %RANDOM
Rwork0.1683 ---
obs0.16975 67801 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.62→70.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 83 212 3662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193573
X-RAY DIFFRACTIONr_bond_other_d0.0010.023525
X-RAY DIFFRACTIONr_angle_refined_deg2.341.9974847
X-RAY DIFFRACTIONr_angle_other_deg0.98438114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38924.172151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8261529
X-RAY DIFFRACTIONr_chiral_restr0.1370.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3612.1161803
X-RAY DIFFRACTIONr_mcbond_other2.3582.1141802
X-RAY DIFFRACTIONr_mcangle_it3.1623.1682260
X-RAY DIFFRACTIONr_mcangle_other3.1623.1712261
X-RAY DIFFRACTIONr_scbond_it4.232.6451770
X-RAY DIFFRACTIONr_scbond_other4.2252.6451770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2773.7552579
X-RAY DIFFRACTIONr_long_range_B_refined7.25118.0634079
X-RAY DIFFRACTIONr_long_range_B_other7.21417.8794013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.617→1.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 245 -
Rwork0.283 4502 -
obs--90.08 %

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