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- PDB-4k8d: Crystal structure of the C558(464)A/C559(465)A double mutant of T... -

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Basic information

Entry
Database: PDB / ID: 4k8d
TitleCrystal structure of the C558(464)A/C559(465)A double mutant of Tn501 MerA in complex with NADPH and Hg2+
ComponentsMercuric reductaseMercury(II) reductase
KeywordsOXIDOREDUCTASE / mercuric ion reductase / flavoenzyme / mercuric ion complex / NADPH complex / ternary complex / reduced form
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 / Chem-NDP / Mercuric reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsDong, A. / Falkowski, M. / Malone, M. / Miller, S.M. / Pai, E.F.
CitationJournal: to be published
Title: Crystal structure of the C136(42)A/C141(47)A double mutant of Tn501 MerA in complex with NADPH and Hg2+
Authors: Dong, A. / Falkowski, M. / Malone, M. / Miller, S.M. / Pai, E.F.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,97724
Polymers49,1621
Non-polymers1,81523
Water7,026390
1
A: Mercuric reductase
hetero molecules

A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,95448
Polymers98,3232
Non-polymers3,63046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area14680 Å2
ΔGint-112 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.922, 86.922, 137.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-506-

UNX

21A-669-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49161.688 Da / Num. of mol.: 1 / Fragment: unp residues 96-561 / Mutation: C136A, C141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: merA / Plasmid: pET3d:cmerA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)pLysS / References: UniProt: P00392, mercury(II) reductase

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Non-polymers , 6 types, 413 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 2.0M AMMONIA Sulfate, 0.1M Tris, pH 9.4, vapor diffusion hanging drop, 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: Nov 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.86→60 Å / Num. obs: 45046 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 32.8
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 4 / Rsym value: 0.561 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GRS

3grs


Resolution: 1.86→28.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.347 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20342 923 2.1 %RANDOM
Rwork0.16742 ---
obs0.16815 44048 99.9 %-
all-45046 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.86 Å2-0 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.86→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 135 390 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193633
X-RAY DIFFRACTIONr_bond_other_d0.0010.023456
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9994984
X-RAY DIFFRACTIONr_angle_other_deg0.74937919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19524.056143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6241527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
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_it1.422.551881
X-RAY DIFFRACTIONr_mcbond_other1.4172.5481880
X-RAY DIFFRACTIONr_mcangle_it2.313.8182354
X-RAY DIFFRACTIONr_scbond_it1.7662.7221752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.858→1.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 62 -
Rwork0.215 3195 -
obs--99.94 %

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