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- PDB-4nb4: Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 4nb4
TitlePantothenamide-bound Pantothenate kinase from Staphylococcus aureus
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE / Protein-Substrate Complex
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / 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-SH3 / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsHughes, S.J. / Antoshchenko, T. / Smil, D. / Park, H.W.
CitationJournal: Proteins / Year: 2014
Title: Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus.
Authors: Hughes, S.J. / Antoshchenko, T. / Kim, K.P. / Smil, D. / Park, H.W.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Type II pantothenate kinase
B: Type II pantothenate kinase
C: Type II pantothenate kinase
D: Type II pantothenate kinase
E: Type II pantothenate kinase
F: Type II pantothenate kinase
G: Type II pantothenate kinase
H: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,80232
Polymers250,6188
Non-polymers7,18324
Water8,305461
1
A: Type II pantothenate kinase
B: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4508
Polymers62,6552
Non-polymers1,7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-79 kcal/mol
Surface area21280 Å2
MethodPISA
2
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4508
Polymers62,6552
Non-polymers1,7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-78 kcal/mol
Surface area21440 Å2
MethodPISA
3
E: Type II pantothenate kinase
F: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4508
Polymers62,6552
Non-polymers1,7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-78 kcal/mol
Surface area21310 Å2
MethodPISA
4
G: Type II pantothenate kinase
H: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4508
Polymers62,6552
Non-polymers1,7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-79 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.010, 70.740, 143.115
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21D
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 16 - 23 / Label seq-ID: 34 - 41

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11FF
21DD
12CC
22DD

NCS ensembles :
ID
1
2

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Components

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


Mass: 31327.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: CoaA, coaW / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G7I0, pantothenate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SH3 / N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 446.389 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H27N2O9P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 0.5 uL protein + 0.5 uL buffer (1.4 M sodium citrate, 0.1 M HEPES, 5% ethylene glycol), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 28, 2013
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 97518 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.094 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.301 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWS

2ews


Resolution: 2.25→39.91 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.832 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.804 / SU ML: 0.223 / SU R Cruickshank DPI: 0.4497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.284 4896 5 %RANDOM
Rwork0.23 ---
obs0.233 97508 99.3 %-
all-98141 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.38 Å2
2---0.5 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16199 0 464 461 17124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917063
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216217
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.97723185
X-RAY DIFFRACTIONr_angle_other_deg0.8153.00537170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00952123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2625.233772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.228152778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2171566
X-RAY DIFFRACTIONr_chiral_restr0.0560.22618
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023947
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_it0.7082.2228501
X-RAY DIFFRACTIONr_mcbond_other0.7082.2228500
X-RAY DIFFRACTIONr_mcangle_it1.2823.32610621
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1F81medium positional0.010.5
2C81medium positional0.010.5
1F48tight thermal2.070.5
2C48tight thermal7.940.5
1F81medium thermal2.472
2C81medium thermal8.192
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 338 -
Rwork0.268 6800 -
obs--99.19 %

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