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- PDB-5x1y: Structure of mercuric reductase from Lysinibacillus sphaericus -

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Basic information

Entry
Database: PDB / ID: 5x1y
TitleStructure of mercuric reductase from Lysinibacillus sphaericus
ComponentsMercuric reductase
KeywordsOXIDOREDUCTASE / Mercuric reductase / merA / 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 / metal ion transport / mercury ion binding / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Mercury(II) reductase / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain ...Mercury(II) reductase / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / 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 speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsKhan, F. / Suguna, K.
CitationJournal: Biometals / Year: 2017
Title: Structural and functional characterization of mercuric reductase from Lysinibacillus sphaericus strain G1.
Authors: Bafana, A. / Khan, F. / Suguna, K.
History
DepositionJan 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mercuric reductase
A: Mercuric reductase
C: Mercuric reductase
D: Mercuric reductase
E: Mercuric reductase
F: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,90912
Polymers359,1956
Non-polymers4,7136
Water00
1
B: Mercuric reductase
C: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3034
Polymers119,7322
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-69 kcal/mol
Surface area32880 Å2
MethodPISA
2
A: Mercuric reductase
E: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3034
Polymers119,7322
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-69 kcal/mol
Surface area33410 Å2
MethodPISA
3
D: Mercuric reductase
F: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3034
Polymers119,7322
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-69 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.380, 150.270, 122.780
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Mercuric reductase / Hg(II) reductase


Mass: 59865.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The protein N-terminus got cleaved during crystallization and the electron density for few C-terminus residues is missing .
Source: (gene. exp.) Lysinibacillus sphaericus (bacteria) / Gene: merA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D9J041, mercury(II) reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 7
Details: 5% v/v Tascimate, 0.1 M HEPES, pH 7.0 and 10% w/v PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.48→87.072 Å / Num. obs: 55103 / % possible obs: 100 % / Redundancy: 11 % / Net I/σ(I): 18.93

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZK7

1zk7


Resolution: 3.48→87.072 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2760 5.01 %
Rwork0.1913 --
obs0.1937 55045 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.48→87.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19777 0 318 0 20095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320378
X-RAY DIFFRACTIONf_angle_d0.61927765
X-RAY DIFFRACTIONf_dihedral_angle_d12.1712179
X-RAY DIFFRACTIONf_chiral_restr0.0423437
X-RAY DIFFRACTIONf_plane_restr0.0033492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.48-3.540.29861110.2432643X-RAY DIFFRACTION100
3.54-3.60440.35121270.24412629X-RAY DIFFRACTION100
3.6044-3.67370.30241120.24992599X-RAY DIFFRACTION100
3.6737-3.74870.26651300.23792620X-RAY DIFFRACTION100
3.7487-3.83020.25511320.2232611X-RAY DIFFRACTION100
3.8302-3.91930.27391360.22672585X-RAY DIFFRACTION100
3.9193-4.01730.25891210.21112640X-RAY DIFFRACTION100
4.0173-4.1260.2731410.20792609X-RAY DIFFRACTION100
4.126-4.24740.28581350.2012637X-RAY DIFFRACTION100
4.2474-4.38450.23591290.17572600X-RAY DIFFRACTION100
4.3845-4.54120.21041340.16892605X-RAY DIFFRACTION100
4.5412-4.7230.20291340.16292611X-RAY DIFFRACTION100
4.723-4.93790.20791810.15492554X-RAY DIFFRACTION100
4.9379-5.19820.20321590.16492593X-RAY DIFFRACTION100
5.1982-5.52380.26991460.18742618X-RAY DIFFRACTION100
5.5238-5.95020.23591650.20532590X-RAY DIFFRACTION100
5.9502-6.54890.26431540.18592612X-RAY DIFFRACTION100
6.5489-7.4960.22041430.17582615X-RAY DIFFRACTION100
7.496-9.44240.17521440.14512651X-RAY DIFFRACTION100
9.4424-87.09950.22191260.18782663X-RAY DIFFRACTION98

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