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- PDB-8ajj: Crystal structure of the disulfide reductase MerA from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 8ajj
TitleCrystal structure of the disulfide reductase MerA from Staphylococcus aureus
ComponentsDihydrolipoamide dehydrogenase
KeywordsOXIDOREDUCTASE / MerA / disulfide reductase
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 / Oxidoreductases / nucleotide binding
Similarity search - Function
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 ...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 / HISTIDINE / Dihydrolipoamide dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWeiland, P. / Altegoer, F. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Microbiol. / Year: 2023
Title: MerA functions as a hypothiocyanous acid reductase and defense mechanism in Staphylococcus aureus.
Authors: Shearer, H.L. / Loi, V.V. / Weiland, P. / Bange, G. / Altegoer, F. / Hampton, M.B. / Antelmann, H. / Dickerhof, N.
History
DepositionJul 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Dihydrolipoamide dehydrogenase
A: Dihydrolipoamide dehydrogenase
B: Dihydrolipoamide dehydrogenase
D: Dihydrolipoamide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,59110
Polymers197,1364
Non-polymers3,4556
Water2,198122
1
C: Dihydrolipoamide dehydrogenase
D: Dihydrolipoamide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1394
Polymers98,5682
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-36 kcal/mol
Surface area34460 Å2
MethodPISA
2
A: Dihydrolipoamide dehydrogenase
hetero molecules

A: Dihydrolipoamide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7648
Polymers98,5682
Non-polymers2,1966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area7750 Å2
ΔGint-49 kcal/mol
Surface area34760 Å2
MethodPISA
3
B: Dihydrolipoamide dehydrogenase
hetero molecules

B: Dihydrolipoamide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1394
Polymers98,5682
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6190 Å2
ΔGint-27 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.630, 250.630, 141.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein
Dihydrolipoamide dehydrogenase / FAD-containing oxidoreductase / Mercuric reductase / Putative pyridine nucleotide-disulfide ...FAD-containing oxidoreductase / Mercuric reductase / Putative pyridine nucleotide-disulfide oxidoreductase / Pyridine nucleotide-disulfide oxidoreductase family protein


Mass: 49284.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: merA, merA_1, merA_6, EDCC5055_00565, EP54_03600, EQ90_11215, GO814_00050, GO942_12510, GQX37_07850, NCTC10702_01041, SAGV69_02028, SAHC1335_01462, SAMEA70146418_00891
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A266CGC0, mercury(II) reductase, Oxidoreductases
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate pH 4.0, 5 % PEG 6000; pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→49.8 Å / Num. obs: 101104 / % possible obs: 99.96 % / Redundancy: 40.5 % / Biso Wilson estimate: 61.17 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.249 / Net I/σ(I): 19.01
Reflection shellResolution: 2.4→2.489 Å / Redundancy: 41.5 % / Rmerge(I) obs: 4.596 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 9949 / CC1/2: 0.365 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBD

1ebd


Resolution: 2.4→49.8 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 5054 5 %
Rwork0.2091 96028 -
obs0.2106 101082 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13049 0 232 122 13403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003213561
X-RAY DIFFRACTIONf_angle_d0.608218483
X-RAY DIFFRACTIONf_chiral_restr0.04682127
X-RAY DIFFRACTIONf_plane_restr0.00412381
X-RAY DIFFRACTIONf_dihedral_angle_d12.88721797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.40611650.41573146X-RAY DIFFRACTION99.85
2.43-2.460.39071680.37523178X-RAY DIFFRACTION100
2.46-2.490.39671640.34873126X-RAY DIFFRACTION100
2.49-2.520.3211670.3283176X-RAY DIFFRACTION100
2.52-2.550.32281670.29023159X-RAY DIFFRACTION99.97
2.55-2.590.30811660.2913159X-RAY DIFFRACTION99.94
2.59-2.630.30911650.2763142X-RAY DIFFRACTION100
2.63-2.660.31651680.26633187X-RAY DIFFRACTION100
2.66-2.710.34841660.28043148X-RAY DIFFRACTION99.94
2.71-2.750.31871670.28523179X-RAY DIFFRACTION100
2.75-2.80.31991660.29353151X-RAY DIFFRACTION100
2.8-2.850.35391680.31043198X-RAY DIFFRACTION100
2.85-2.90.38841660.29983149X-RAY DIFFRACTION99.91
2.9-2.960.32081670.29583182X-RAY DIFFRACTION100
2.96-3.030.36021680.25913183X-RAY DIFFRACTION100
3.03-3.10.29581670.24713178X-RAY DIFFRACTION100
3.1-3.180.33041680.2453189X-RAY DIFFRACTION100
3.18-3.260.26131670.22083180X-RAY DIFFRACTION100
3.26-3.360.23291680.22623183X-RAY DIFFRACTION100
3.36-3.470.28071690.23353203X-RAY DIFFRACTION100
3.47-3.590.25271680.21233199X-RAY DIFFRACTION100
3.59-3.730.22321680.20273197X-RAY DIFFRACTION100
3.73-3.90.21121690.19273200X-RAY DIFFRACTION100
3.9-4.110.2161700.17323234X-RAY DIFFRACTION100
4.11-4.370.19571690.16613209X-RAY DIFFRACTION100
4.37-4.70.17851700.14673244X-RAY DIFFRACTION100
4.7-5.180.17011720.15963259X-RAY DIFFRACTION100
5.18-5.920.241730.19153277X-RAY DIFFRACTION100
5.92-7.460.19741740.19723322X-RAY DIFFRACTION100
7.46-49.80.16921840.16753491X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.637635338191.39599560107-0.5697135001111.54445395754-0.1153003775330.7395233910510.276960172756-0.466061041162-0.2242753769710.41519068155-0.253067380642-0.2930950279950.08348760945160.355036904532-0.02497408370380.511810857240.04466604553580.02092290789650.59109206896-0.08887119403130.481511608012-24.362274538-80.08831431944.88559709583
21.995476212270.06037866037320.6415463486691.81512708628-0.4427753899551.91469674526-0.2527522415430.1681426668270.6745370451560.06911912299910.0231426753283-0.413699075854-0.7085587841950.4920944142410.1347745990720.587702208822-0.137114949271-0.02438450395720.529344001835-0.03733145019880.73531849667222.9772404178-46.6691550136-32.8386517979
30.775300926975-0.3205125316580.1314428748561.14497530518-0.6248932961981.16180951736-0.0764413862944-0.11954698425-0.07362658209070.03935099605330.029525557774-0.1644022489110.1396273491520.2038195776730.06217428051130.3890025435940.02746968897510.05679755092510.4764669850.007010194463510.46679340097623.756183388-85.0942449842-29.4918796609
41.59509208079-0.3502576366460.2567863700831.259349207670.1350044314330.9480107942520.0730275161772-0.0809853286757-0.08011021438950.07045090040870.04688810873570.346956233065-0.118048914909-0.383778280351-0.1127363512580.5434371933570.123927246580.01080162194740.5768421922410.09225539968340.48593439244644.3781248744-115.0185323972.31015530973
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 5 through 445)BF5 - 4451 - 391
22(chain 'D' and resid 3 through 445)DH3 - 4451 - 397
33(chain 'C' and resid 3 through 446)CA3 - 4461 - 444
44(chain 'A' and resid 3 through 444)AC3 - 4441 - 442

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