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- PDB-8k40: mercuric reductase,GbsMerA, - FAD bound -

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Basic information

Entry
Database: PDB / ID: 8k40
Titlemercuric reductase,GbsMerA, - FAD bound
ComponentsNAD(P)/FAD-dependent oxidoreductase
KeywordsTRANSFERASE / Mercuric reductase / Gelidibacter salicanalis PAMC21136 / Hg resistance / Heavy metal detoxification
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase, class I / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)/FAD-dependent oxidoreductase
Similarity search - Component
Biological speciesGelidibacter salicanalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDo, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentPM23030 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2023
Title: Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136.
Authors: Pardhe, B.D. / Lee, M.J. / Lee, J.H. / Do, H. / Oh, T.J.
History
DepositionJul 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)/FAD-dependent oxidoreductase
B: NAD(P)/FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4784
Polymers99,9072
Non-polymers1,5712
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-71 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.190, 105.820, 126.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD(P)/FAD-dependent oxidoreductase


Mass: 49953.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gelidibacter salicanalis (bacteria) / Gene: JEM65_00875 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A934NG65
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 53.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.6 M sodium phosphate monobasic/0.4 M potassium phosphate dibasic, 0.1 M sodium phosphate dibasic/citric acid (pH 4.2)]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→29.38 Å / Num. obs: 33032 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.6 / Num. unique obs: 3967 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.984 / SU ML: 0.306 / Cross valid method: FREE R-VALUE / ESU R: 0.847 / ESU R Free: 0.354
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2818 2000 6.055 %
Rwork0.2192 31028 -
all0.223 --
obs-33028 99.885 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 78.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.021 Å2-0 Å20 Å2
2--0.034 Å2-0 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 106 33 6937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176688
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6459545
X-RAY DIFFRACTIONr_angle_other_deg1.2211.57815566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06223.475305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.732151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8651526
X-RAY DIFFRACTIONr_chiral_restr0.0610.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_nbd_refined0.1970.21270
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26066
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23325
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.28
X-RAY DIFFRACTIONr_nbd_other0.210.217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.21
X-RAY DIFFRACTIONr_mcbond_it6.3558.2143524
X-RAY DIFFRACTIONr_mcbond_other6.3558.2143523
X-RAY DIFFRACTIONr_mcangle_it9.22812.3134398
X-RAY DIFFRACTIONr_mcangle_other9.22712.3134399
X-RAY DIFFRACTIONr_scbond_it5.8068.6633527
X-RAY DIFFRACTIONr_scbond_other5.8058.6643524
X-RAY DIFFRACTIONr_scangle_it8.85712.7585147
X-RAY DIFFRACTIONr_scangle_other8.85612.7575148
X-RAY DIFFRACTIONr_lrange_it13.614156.99628315
X-RAY DIFFRACTIONr_lrange_other13.615157.00628311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.3531450.2962244X-RAY DIFFRACTION100
2.668-2.7410.4011420.3272212X-RAY DIFFRACTION100
2.741-2.820.4171380.3342147X-RAY DIFFRACTION100
2.82-2.9070.3621350.3012085X-RAY DIFFRACTION100
2.907-3.0020.3241320.3072040X-RAY DIFFRACTION99.954
3.002-3.1070.3531250.281955X-RAY DIFFRACTION100
3.107-3.2240.3151210.2551867X-RAY DIFFRACTION99.9497
3.224-3.3560.3331180.2761826X-RAY DIFFRACTION99.9486
3.356-3.5040.2811130.2471763X-RAY DIFFRACTION100
3.504-3.6750.3411080.2581684X-RAY DIFFRACTION100
3.675-3.8740.2931040.2311598X-RAY DIFFRACTION99.9413
3.874-4.1080.307990.221533X-RAY DIFFRACTION100
4.108-4.3910.193910.1761424X-RAY DIFFRACTION100
4.391-4.7410.245860.1831323X-RAY DIFFRACTION100
4.741-5.1920.265800.1771254X-RAY DIFFRACTION100
5.192-5.8020.279730.1931121X-RAY DIFFRACTION100
5.802-6.6940.284660.1891016X-RAY DIFFRACTION100
6.694-8.1840.21540.162859X-RAY DIFFRACTION100
8.184-11.5160.191450.152690X-RAY DIFFRACTION100
11.516-23.3990.31250.283387X-RAY DIFFRACTION92.3767

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