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- PDB-4emw: Crystal Structure of Staphylococcus aureus bound with the covalen... -

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Basic information

Entry
Database: PDB / ID: 4emw
TitleCrystal Structure of Staphylococcus aureus bound with the covalent inhibitor EtVC-CoA
ComponentsCoenzyme A disulfide reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
Function / homology
Function and homology information


CoA-disulfide reductase / CoA-disulfide reductase (NADPH) activity / protein disulfide isomerase activity / NADP binding / flavin adenine dinucleotide 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 / FAD/NAD(P)-binding domain ...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
Chem-CAJ / FLAVIN-ADENINE DINUCLEOTIDE / Coenzyme A disulfide reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.39 Å
AuthorsEdwards, J.S. / Wallace, B.D. / 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 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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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)101,5059
Polymers98,1792
Non-polymers3,3267
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-57 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.036, 64.885, 94.392
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 49089.336 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 225 molecules

#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-CAJ / ethyl 5-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]pentanoate


Mass: 835.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H44N7O18P3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COA MIMIC INHIBITOR CAJ IS BOUND AT CYS 43 WITH A COVALENT BOND BETWEE CBU AOF CA6 AND SG OF ...THE COA MIMIC INHIBITOR CAJ IS BOUND AT CYS 43 WITH A COVALENT BOND BETWEE CBU AOF CA6 AND SG OF CYS. THE PRE-REACTION COMPOUND HAD A DOUBLE BOND BETWEEN CBU AND CBV WHICH OPENED UP TO FORM THE COVALENT LINKAGE WITH CYS SIDE CHAIN UPON REACTION.

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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: 2.29 Å3/Da / Density % sol: 46.36 %
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, EtVC-CoA, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: Double crystal with K-B biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→91.28 Å / Num. obs: 34628 / % possible obs: 98.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.446.40.401197
2.44-2.496.50.381196.4
2.49-2.536.70.369196.8
2.53-2.5970.348197.2
2.59-2.647.20.333197
2.64-2.77.20.478197.5
2.7-2.777.40.275197
2.77-2.857.50.238197.8
2.85-2.937.50.218197.7
2.93-3.027.60.19197.8
3.02-3.137.60.168198.5
3.13-3.267.60.151198.6
3.26-3.417.60.138198.5
3.41-3.587.60.154198.8
3.58-3.817.30.146199
3.81-4.17.30.123199
4.1-4.527.40.085199
4.52-5.177.40.077198.9
5.17-6.517.50.075199.3
6.51-507.20.105199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.39→91.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.867 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21841 1709 5 %RANDOM
Rwork0.16432 ---
obs0.167 32753 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.669 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.19 Å2
2--4.04 Å2-0 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.39→91.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 217 218 7240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.999797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43624.495327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.649151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5551539
X-RAY DIFFRACTIONr_chiral_restr0.1110.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215403
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.389→2.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 98 -
Rwork0.187 2095 -
obs--86.71 %

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