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- PDB-4eqr: Crystal structure of the Y361F mutant of Staphylococcus aureus CoADR -

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Basic information

Entry
Database: PDB / ID: 4eqr
TitleCrystal structure of the Y361F 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 / Resolution: 1.8 Å
AuthorsWallace, B.D. / Edwards, J.S. / 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 1.1Oct 16, 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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)101,79715
Polymers98,4052
Non-polymers3,39213
Water21,9061216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-110 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.880, 65.090, 94.410
Angle α, β, γ (deg.)90.000, 104.720, 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: 49202.516 Da / Num. of mol.: 2 / Mutation: Y361F
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, 1229 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.: 1216 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
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: 100 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: 1.8→53 Å / Num. obs: 160762 / % possible obs: 99.9 % / Redundancy: 7.07 % / Rmerge(I) obs: 0.104 / Χ2: 0.96 / Net I/σ(I): 7.9 / Scaling rejects: 4410
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.866.850.4592.75614582001.18100
1.86-1.946.910.40135710282581.13100
1.94-2.036.940.3223.85688981941.1100
2.03-2.136.980.2654.45751082390.99100
2.13-2.276.930.2115.25708082230.95100
2.27-2.4470.1676.55784782500.93100
2.44-2.697.170.1427.55944682740.9100
2.69-3.087.340.1159.46097182700.87100
3.08-3.887.380.07314.66201182920.7799.8
3.88-537.170.05221.16298083750.8599

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Processing

Software
NameVersionClassificationNB
d*TREK9.1Ldata scaling
d*TREK9.1Ldata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.258 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.8415 / SU ML: 0.47 / σ(F): 0.66 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 4081 4.97 %random
Rwork0.1847 ---
obs0.1867 82317 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.991 Å2 / ksol: 0.432 e/Å3
Displacement parametersBiso max: 82.17 Å2 / Biso mean: 24.756 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.8572 Å20 Å21.8803 Å2
2--5.1121 Å2-0 Å2
3----4.255 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 211 1216 8357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067389
X-RAY DIFFRACTIONf_angle_d1.04710056
X-RAY DIFFRACTIONf_chiral_restr0.0711088
X-RAY DIFFRACTIONf_plane_restr0.0081276
X-RAY DIFFRACTIONf_dihedral_angle_d18.7462865
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 (%)
1.8-1.82040.31482590.25295128538799
1.8204-1.84180.31382610.256250815342100
1.8418-1.86430.30192860.24715045533199
1.8643-1.88790.24452620.23645146540899
1.8879-1.91270.24572670.22251355402100
1.9127-1.93890.27272130.21995150536399
1.9389-1.96660.26232780.21225076535499
1.9666-1.99590.27662450.21325121536699
1.9959-2.02710.25152640.20535047531199
2.0271-2.06030.2732850.19851295414100
2.0603-2.09580.24062600.20451315391100
2.0958-2.13390.24942790.195350595338100
2.1339-2.17490.21812640.19185179544399
2.1749-2.21920.24552550.18950355290100
2.2192-2.26750.21672460.181451205366100
2.2675-2.32010.24512720.183251815453100
2.3201-2.37810.23872690.180850855354100
2.3781-2.44230.25112660.187451055371100
2.4423-2.51410.25263030.18850675370100
2.5141-2.59510.24442680.189851085376100
2.5951-2.68770.24252650.192851495414100
2.6877-2.79520.2642790.19445072535199
2.7952-2.92210.21012860.19065040532699
2.9221-3.07580.2522930.19065074536799
3.0758-3.26790.2072540.168851625416100
3.2679-3.51930.17542390.141150745313100
3.5193-3.87180.16512670.13815121538899
3.8718-4.42830.16412830.13785064534799
4.4283-5.56470.1552720.13665018529098
5.5647-22.260.22442540.18554866512095

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