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- PDB-4gi7: Crystal structure of Klebsiella pneumoniae pantothenate kinase in... -

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Basic information

Entry
Database: PDB / ID: 4gi7
TitleCrystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue
ComponentsPantothenate kinase
KeywordsTRANSFERASE / protein-substrate complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDE / Chem-0JR / ADENOSINE-5'-DIPHOSPHATE / Pantothenate kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.95 Å
AuthorsLi, B. / Tempel, W. / Smil, D. / Bolshan, Y. / Hong, B.S. / Park, H.W. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2013
Title: Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides.
Authors: Li, B. / Tempel, W. / Smil, D. / Bolshan, Y. / Schapira, M. / Park, H.W.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Pantothenate kinase
C: Pantothenate kinase
B: Pantothenate kinase
D: Pantothenate kinase
E: Pantothenate kinase
F: Pantothenate kinase
G: Pantothenate kinase
H: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,65166
Polymers307,6868
Non-polymers4,96458
Water18,4291023
1
A: Pantothenate kinase
C: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,39517
Polymers76,9222
Non-polymers1,47315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-40 kcal/mol
Surface area26120 Å2
MethodPISA
2
B: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,39519
Polymers76,9222
Non-polymers1,47317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-40 kcal/mol
Surface area26310 Å2
MethodPISA
3
E: Pantothenate kinase
F: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08515
Polymers76,9222
Non-polymers1,16413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-39 kcal/mol
Surface area26380 Å2
MethodPISA
4
G: Pantothenate kinase
H: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,77615
Polymers76,9222
Non-polymers85413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-37 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.928, 130.938, 193.022
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pantothenate kinase / Pantothenic acid kinase


Mass: 38460.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 342 / Gene: coaA, KPK_5321 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5XYG3, 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-0JR / (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide


Type: Non-polymer / Class: Antibiotic, Antimicrobial / Mass: 309.361 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H23N3O4
References: (2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDE
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 45 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1023 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5 uL protein + 0.5 uL buffer (20% PEG3350, 0.2 M tri-lithium citrate, pH 7.0) + 0.2 uL 40% 2,5-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03321 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 235112 / Num. obs: 234904 / % possible obs: 99.86 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.2755
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.95-2.066.360.8521466633760199.11
2.06-2.186.80.54219671323221100
2.18-2.337.020.36212676302841100
2.33-2.527.230.26204773283141100
2.52-2.767.390.18192637260651100
2.76-3.087.490.13177139236431100
3.08-3.567.50.1157182209461100
3.56-4.367.430.09132273178081100
4.36-6.177.340.0810192913885199.99
6.17-4070.08551317877199.61

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementResolution: 1.95→39.681 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Matrix type: sparse / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.465 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 11741 5.004 %RANDOM
Rwork0.186 222889 --
obs0.188 234630 99.778 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 115.61 Å2 / Biso mean: 33.063 Å2 / Biso min: 12.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.596 Å20 Å20 Å2
2---0.639 Å2-0 Å2
3---1.236 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19893 0 371 1023 21287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219799
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9828152
X-RAY DIFFRACTIONr_angle_other_deg0.7883.00245502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80952451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05523.72965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.616153558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.21515143
X-RAY DIFFRACTIONr_chiral_restr0.0760.23146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024838
X-RAY DIFFRACTIONr_mcbond_it2.0293.1329828
X-RAY DIFFRACTIONr_mcbond_other2.0293.1329827
X-RAY DIFFRACTIONr_mcangle_it3.1444.68712268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.95-2.0010.3358070.287160900.291720498.2160.284
2.001-2.0550.2828460.245159420.2471679299.9760.238
2.055-2.1150.2758030.226154760.2281628599.9630.214
2.115-2.180.2578050.215151140.2171592799.950.201
2.18-2.2510.2547890.207145380.211533899.9280.193
2.251-2.3290.2577600.198141070.2011488099.9130.182
2.329-2.4170.2557400.203136880.2061444399.8960.187
2.417-2.5150.2547240.201130870.2031382199.9280.186
2.515-2.6270.2386940.194126060.1971331299.910.182
2.627-2.7540.2456180.197120840.21270999.9450.186
2.754-2.9030.2296010.19115270.1921214099.9010.183
2.903-3.0780.2335630.194109040.1961147899.9040.191
3.078-3.2890.2225380.198103040.21084899.9450.199
3.289-3.550.2144970.18895920.191009999.9010.194
3.55-3.8860.1864580.1788570.171932499.9030.182
3.886-4.3390.1724030.14880640.149847299.9410.163
4.339-5.0010.1653650.14271310.143750399.9070.16
5.001-6.1010.1923180.16861130.169643999.8760.186
6.101-8.5270.2012600.1747930.171506399.8020.191
8.527-39.6810.1591520.14128730.142303699.6380.171

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