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- PDB-4eqx: Crystal Structure of the C43S Mutant of Staphylococcus aureus CoADR -

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Basic information

Entry
Database: PDB / ID: 4eqx
TitleCrystal Structure of the C43S Mutant of Staphylococcus aureus CoADR
ComponentsCoenzyme A disulfide reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


CoA-disulfide reductase / CoA-disulfide reductase (NADPH) activity / protein disulfide isomerase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Coenzyme A disulphide reductase, staphyolococci / Coenzyme A disulphide reductase / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 ...Coenzyme A disulphide reductase, staphyolococci / Coenzyme A disulphide reductase / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Coenzyme A disulfide reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEdwards, J.S. / Wallace, B.D. / Wallen, J.R. / Claiborne, A. / Redinbo, M.R.
CitationJournal: Biochemistry / Year: 2012
Title: Turnover-Dependent Covalent Inactivation of Staphylococcus aureus Coenzyme A-Disulfide Reductase by Coenzyme A-Mimetics: Mechanistic and Structural Insights.
Authors: Wallace, B.D. / Edwards, J.S. / Wallen, J.R. / Moolman, W.J. / van der Westhuyzen, R. / Strauss, E. / Redinbo, M.R. / Claiborne, A.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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: Coenzyme A disulfide reductase
B: Coenzyme A disulfide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,16610
Polymers98,4052
Non-polymers1,7628
Water16,916939
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-92 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.960, 65.380, 94.470
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coenzyme A disulfide reductase / CoA-disulfide reductase / CoADR


Mass: 49202.449 Da / Num. of mol.: 2 / Mutation: C43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: USA300 / Gene: cdr, SAUSA300_0873 / Plasmid: T7, pXCDR / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (de3) / References: UniProt: Q2FIA5, CoA-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 400, magnesium chloride, HEPES, NADP+, pH 7.2, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2008
RadiationMonochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing 3.3:1 demagnification. Mirror: ...Monochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→53.16 Å / Num. obs: 98511 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Χ2: 1 / Net I/σ(I): 11 / Scaling rejects: 4694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.764.270.363.14217298241.2899.9
1.76-1.835.050.313.64955597681.2499.9
1.83-1.915.820.2694.35755398191.2499.9
1.91-2.026.880.2185.36797898121.18100
2.02-2.146.940.1686.76814397651.0799.9
2.14-2.316.730.1268.76669398600.98100
2.31-2.546.720.10110.26654998460.91100
2.54-2.917.060.08112.86999798600.83100
2.91-3.666.980.05818.56968699160.76100
3.66-53.166.590.03830.667430100410.7499.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
d*TREK9.2Ldata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.309 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 4891 5 %RANDOM
Rwork0.1934 ---
obs0.1954 97663 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.7 Å2 / Biso mean: 22.812 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.06 Å2
2---0.25 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 112 939 7983
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 360 -
Rwork0.263 6890 -
all-7250 -
obs--99.66 %

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