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- PDB-4eqw: Crystal Structure of the Y361F, Y419F Mutant of Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 4eqw
TitleCrystal Structure of the Y361F, Y419F 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 / 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 ...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
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Coenzyme A disulfide reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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

Downloads & links

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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)101,76515
Polymers98,3732
Non-polymers3,39213
Water23,1491285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-111 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 65.520, 94.710
Angle α, β, γ (deg.)90.000, 104.780, 90.000
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: 49186.516 Da / Num. of mol.: 2 / Mutation: Y361F, Y419F
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, 1298 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.07 %
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 at 3.3:1 demagnification. ...Monochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 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: 1.5→53.29 Å / Num. obs: 140142 / % possible obs: 97.1 % / Redundancy: 6.92 % / Rmerge(I) obs: 0.063 / Χ2: 0.89 / Net I/σ(I): 16 / Scaling rejects: 27032
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.5-1.555.20.2944.161505111410.8677.5
1.55-1.626.150.2565.389930138020.9396.2
1.62-1.697.010.2116.5104555143600.81100
1.69-1.787.090.1678104956143710.75100
1.78-1.897.150.13210.1105485143860.79100
1.89-2.047.250.10413.3105999143650.83100
2.04-2.247.310.0817.2106939144660.83100
2.24-2.567.350.06522.3107435144330.86100
2.56-3.237.40.05627.6108410144760.94100
3.23-53.296.90.04538.6102010143421.2797.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.1Ldata scaling
d*TREK9.1Ldata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.125 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8705 / SU ML: 0.32 / σ(F): 1.37 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 13446 9.63 %random
Rwork0.18 ---
obs0.1826 140124 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.748 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 72.44 Å2 / Biso mean: 21.6408 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.3516 Å20 Å22.5021 Å2
2--4.2626 Å2-0 Å2
3----3.911 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 211 1285 8424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057387
X-RAY DIFFRACTIONf_angle_d1.02710052
X-RAY DIFFRACTIONf_chiral_restr0.071088
X-RAY DIFFRACTIONf_plane_restr0.0061274
X-RAY DIFFRACTIONf_dihedral_angle_d20.4552873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.27476330.26775988662170
1.517-1.53490.28097460.25516344709075
1.5349-1.55360.28427550.24696947770281
1.5536-1.57330.27228020.23947504830689
1.5733-1.5940.25858860.22268328921497
1.594-1.61580.24819180.20878484940299
1.6158-1.63890.2418820.194685359417100
1.6389-1.66330.22249500.194784409390100
1.6633-1.68930.2338610.190286439504100
1.6893-1.7170.21919080.181985449452100
1.717-1.74660.21978220.176585739395100
1.7466-1.77840.21168650.183286109475100
1.7784-1.81260.22029450.175684759420100
1.8126-1.84960.21038170.184886239440100
1.8496-1.88980.22569130.188185559468100
1.8898-1.93380.22899270.18585509477100
1.9338-1.98210.20439550.176984389393100
1.9821-2.03570.20579050.177484789383100
2.0357-2.09560.20529110.17986149525100
2.0956-2.16320.20178820.17385189400100
2.1632-2.24050.21219310.171785619492100
2.2405-2.33020.22068990.176585609459100
2.3302-2.43620.20889930.178984199412100
2.4362-2.56460.22158710.18685619432100
2.5646-2.72520.21168740.183885549428100
2.7252-2.93550.20479370.180284609397100
2.9355-3.23070.19619520.173884939445100
3.2307-3.69770.17189480.149984729420100
3.6977-4.65660.15128840.13578364924898
4.6566-33.13330.18858180.17277919873792

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