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- PDB-4em4: Crystal Structure of Staphylococcus aureus bound with the covalen... -

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Basic information

Entry
Database: PDB / ID: 4em4
TitleCrystal Structure of Staphylococcus aureus bound with the covalent inhibitor Pethyl-VS-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 / 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
Chem-CA8 / FLAVIN-ADENINE DINUCLEOTIDE / Coenzyme A disulfide reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.821 Å
AuthorsWallace, B.D. / Edwards, J.S. / 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 11, 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 1.2Oct 30, 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_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

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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)102,13716
Polymers98,4372
Non-polymers3,70014
Water19,4561080
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-102 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.144, 64.909, 94.442
Angle α, β, γ (deg.)90.00, 104.62, 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: 49218.516 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, 1094 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA8 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[4-(phenylsulfonyl)butylamino]propyl]amino]butyl] hydrogen phosphate


Mass: 903.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44N7O18P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE COA MIMIC INHIBITOR CA8 IS BOUND AT CYS 43 WITH A COVALENT BOND BETWEE CBU AOF CA6 AND SG OF ...THE COA MIMIC INHIBITOR CA8 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: 46.38 %
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, phenyl-VS-COA

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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: Mar 17, 2011
RadiationMonochromator: double crystal and K-B biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Number: 560054 / Rmerge(I) obs: 0.109 / Χ2: 4.66 / D res high: 1.83 Å / D res low: 50 Å / Num. obs: 76577 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.975098.410.0535.297.4
3.944.9799.310.0647.2817.7
3.443.9498.910.0828.3177.7
3.133.4498.810.0977.9167.7
2.93.1398.710.1096.6547.7
2.732.998.410.1235.9337.7
2.62.7398.210.1395.4057.7
2.482.698.210.1514.837.6
2.392.4897.810.1734.6867.6
2.312.3997.910.1854.4757.6
2.232.3197.210.2014.2557.6
2.172.2397.410.2213.8867.6
2.112.1797.310.2443.4977.5
2.062.1197.110.2713.2017.4
2.012.0696.810.3022.8147.3
1.972.0196.610.3282.6267.1
1.931.9795.610.3562.5296.8
1.91.9394.910.4082.2446.5
1.861.993.610.4472.0236.1
1.831.8689.910.4932.0585.6
ReflectionResolution: 1.8→50 Å / Num. obs: 76527 / % possible obs: 93.14 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 38.14
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.98 / % possible all: 89.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8_1057refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.821→32.455 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 3827 5 %
Rwork0.1535 --
obs0.1563 76527 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→32.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 232 1080 8240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017462
X-RAY DIFFRACTIONf_angle_d1.75810168
X-RAY DIFFRACTIONf_dihedral_angle_d15.2762838
X-RAY DIFFRACTIONf_chiral_restr0.1481133
X-RAY DIFFRACTIONf_plane_restr0.0061295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8215-1.84450.3616790.22521614X-RAY DIFFRACTION58
1.8445-1.86880.25531250.22292552X-RAY DIFFRACTION91
1.8688-1.89440.28361360.20772623X-RAY DIFFRACTION94
1.8944-1.92150.22841370.19872636X-RAY DIFFRACTION94
1.9215-1.95010.21821540.19052684X-RAY DIFFRACTION96
1.9501-1.98060.24341330.18082671X-RAY DIFFRACTION96
1.9806-2.01310.24231440.18252697X-RAY DIFFRACTION96
2.0131-2.04780.20761360.17192711X-RAY DIFFRACTION97
2.0478-2.0850.23221460.17222723X-RAY DIFFRACTION97
2.085-2.12510.20721340.1722721X-RAY DIFFRACTION97
2.1251-2.16850.22371610.16822706X-RAY DIFFRACTION97
2.1685-2.21560.20541590.16462697X-RAY DIFFRACTION97
2.2156-2.26710.24981460.15962718X-RAY DIFFRACTION97
2.2671-2.32380.22161360.16212781X-RAY DIFFRACTION98
2.3238-2.38660.20541230.16422752X-RAY DIFFRACTION98
2.3866-2.45680.21871470.16362732X-RAY DIFFRACTION98
2.4568-2.53610.23251490.16662733X-RAY DIFFRACTION98
2.5361-2.62670.22611460.16142779X-RAY DIFFRACTION98
2.6267-2.73180.20911320.16022758X-RAY DIFFRACTION98
2.7318-2.85610.20411560.15372762X-RAY DIFFRACTION98
2.8561-3.00660.21581410.15872763X-RAY DIFFRACTION99
3.0066-3.19480.22071560.15292785X-RAY DIFFRACTION99
3.1948-3.44120.17651580.13952779X-RAY DIFFRACTION99
3.4412-3.7870.18171410.12892808X-RAY DIFFRACTION99
3.787-4.33390.14861460.12132809X-RAY DIFFRACTION99
4.3339-5.45610.14961370.11862850X-RAY DIFFRACTION99
5.4561-32.45960.20011690.16342856X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 4.6497 Å / Origin y: 8.668 Å / Origin z: 59.1942 Å
111213212223313233
T0.1073 Å2-0.0018 Å2-0.0063 Å2-0.1168 Å2-0.0068 Å2--0.137 Å2
L0.1076 °20.0558 °2-0.0557 °2-0.1665 °2-0.0428 °2--0.3313 °2
S0.0014 Å °-0.0043 Å °0.0064 Å °0.0205 Å °-0.0061 Å °-0.0286 Å °-0.0016 Å °0.043 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 438
2X-RAY DIFFRACTION1allB2 - 438
3X-RAY DIFFRACTION1allE1
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allF1
6X-RAY DIFFRACTION1allD1
7X-RAY DIFFRACTION1allS1 - 1084
8X-RAY DIFFRACTION1allG1 - 3
9X-RAY DIFFRACTION1allI1 - 7

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