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- PDB-1zx9: Crystal Structure of Tn501 MerA -

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Basic information

Entry
Database: PDB / ID: 1zx9
TitleCrystal Structure of Tn501 MerA
ComponentsMercuric reductaseMercury(II) reductase
KeywordsOXIDOREDUCTASE / Mercuric ion reductase
Function / homology
Function and homology information


mercury(II) reductase / mercury (II) reductase activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / detoxification of mercury ion / mercury ion binding / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Mercury(II) reductase / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / 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 ...Mercury(II) reductase / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDong, A. / Ledwidge, R. / Patel, B. / Fiedler, D. / Falkowski, M. / Zelikova, J. / Summers, A.O. / Pai, E.F. / Miller, S.M.
CitationJournal: Biochemistry / Year: 2005
Title: NmerA, the Metal Binding Domain of Mercuric Ion Reductase, Removes Hg(2+) from Proteins, Delivers It to the Catalytic Core, and Protects Cells under Glutathione-Depleted Conditions
Authors: Ledwidge, R. / Patel, B. / Dong, A. / Fiedler, D. / Falkowski, M. / Zelikova, J. / Summers, A.O. / Pai, E.F. / Miller, S.M.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0112
Polymers49,2261
Non-polymers7861
Water3,333185
1
A: Mercuric reductase
hetero molecules

A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0234
Polymers98,4522
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-11
Buried area9200 Å2
ΔGint-52 kcal/mol
Surface area33530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.538, 72.538, 155.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe second part of the biological assembly is generated by the two fold axis: y x -z.

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Components

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


Mass: 49225.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: merA / Plasmid: pJOE114 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00392, mercury(II) reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.1 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6 / Details: PEG 400, pH 4.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2001 / Details: mirror
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 33542 / Num. obs: 30559 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.83 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.853 / Num. unique all: 2789 / Rsym value: 0.362 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3GRS

3grs


Resolution: 1.9→29.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 475661.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1526 5 %RANDOM
Rwork0.215 ---
all0.223 33542 --
obs0.215 30559 50 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5957 Å2 / ksol: 0.339615 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å20 Å20 Å2
2--3.4 Å20 Å2
3----6.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 53 185 3587
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 194 4.4 %
Rwork0.26 4196 -
obs-4390 80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fad_xplor_par.txtfad_xplor_top.txt

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