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- PDB-4k7z: Crystal structure of the C136(42)A/C141(47)A double mutant of Tn5... -

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Basic information

Entry
Database: PDB / ID: 4k7z
TitleCrystal structure of the C136(42)A/C141(47)A double mutant of Tn501 MerA in complex with NADP and Hg2+
ComponentsMercuric 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 (NADP+) activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / detoxification of mercury ion / mercury ion binding / NADP binding / flavin adenine dinucleotide 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 / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Mercuric reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDong, A. / Falkowaski, 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 NADP and Hg2+
Authors: Dong, A. / Falkowski, M. / Malone, M. / Miller, S.M. / Pai, E.F.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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)51,45626
Polymers49,1621
Non-polymers2,29425
Water10,124562
1
A: Mercuric reductase
hetero molecules

A: Mercuric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,91152
Polymers98,3232
Non-polymers4,58850
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area15780 Å2
ΔGint-139 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.584, 86.584, 137.370
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-1130-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49161.680 Da / Num. of mol.: 1 / Fragment: unp residues 96-561 / Mutation: C42A, C47A
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 , 7 types, 587 molecules

#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 16 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 2.0M AMMONIA Sulfate, 0.1M Tris pH9.4, vapor diffusion hanging drop, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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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: 1.5→80 Å / Num. obs: 83679 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 30
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.74 / Num. unique all: 3831 / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GRS

3grs


Resolution: 1.5→26.87 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.198 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 1658 2 %RANDOM
Rwork0.1812 ---
obs0.1817 83623 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.11 Å2 / Biso mean: 21.3006 Å2 / Biso min: 11.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 151 562 4126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193699
X-RAY DIFFRACTIONr_bond_other_d0.0010.023514
X-RAY DIFFRACTIONr_angle_refined_deg1.2992.0025080
X-RAY DIFFRACTIONr_angle_other_deg0.73738071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01824.384146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52115563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4271526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_mcbond_it0.8671.8821900
X-RAY DIFFRACTIONr_mcbond_other0.8641.8811899
X-RAY DIFFRACTIONr_mcangle_it1.4962.8232382
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 116 -
Rwork0.288 5637 -
all-5753 -
obs--93.76 %

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