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- PDB-6avp: Staphylococcus aureus Type II pantothenate kinase in complex with... -

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Basic information

Entry
Database: PDB / ID: 6avp
TitleStaphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Phosphate-MeO-N5Pan
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Type II pantothenate kinase, bacterial / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-N7E / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
CitationJournal: To Be Published
Title: Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase.
Authors: Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
History
DepositionSep 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II pantothenate kinase
B: Type II pantothenate kinase
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,87416
Polymers115,4754
Non-polymers3,40012
Water3,405189
1
A: Type II pantothenate kinase
C: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4378
Polymers57,7372
Non-polymers1,7006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-79 kcal/mol
Surface area20710 Å2
MethodPISA
2
B: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4378
Polymers57,7372
Non-polymers1,7006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-78 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.571, 56.705, 133.075
Angle α, β, γ (deg.)90.000, 99.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type II pantothenate kinase / PanK-II / Pantothenic acid kinase


Mass: 28868.654 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: coaW, ERS072840_01840, ERS073071_01656, ERS073583_01730, SAMEA2236422_02154, SAMEA2236459_02267, SAMEA2384700_01964, SAMEA2384800_02212, SAMEA2384856_02334, SAMEA2445640_02323
Production host: Escherichia coli (E. coli)
References: UniProt: A0A167Z3Z6, UniProt: Q2FWC7*PLUS, pantothenate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-N7E / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(5-methoxypentyl)-beta-alaninamide


Mass: 398.389 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H31N2O8P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→131.35 Å / Num. obs: 47658 / % possible obs: 99.4 % / Redundancy: 3.49 % / Net I/σ(I): 8.39
Reflection shellHighest resolution: 2.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→131.35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.492 / ESU R Free: 0.299
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 2410 5.1 %RANDOM
Rwork0.2447 ---
obs0.2472 45234 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.57 Å2 / Biso mean: 39.87 Å2 / Biso min: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1-5.39 Å20 Å2-4.69 Å2
2---1.97 Å20 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 2.3→131.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8030 0 216 189 8435
Biso mean--27.14 30.66 -
Num. residues----1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198384
X-RAY DIFFRACTIONr_bond_other_d00.028016
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.97511384
X-RAY DIFFRACTIONr_angle_other_deg3.7743.00518372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37925.213376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.325151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0731532
X-RAY DIFFRACTIONr_chiral_restr0.10.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029558
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021918
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 165 -
Rwork0.387 3262 -
all-3427 -
obs--96.81 %

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