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- PDB-4f7w: Crystal structure of Klebsiella pneumoniae pantothenate kinase in... -

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Basic information

Entry
Database: PDB / ID: 4f7w
TitleCrystal structure of Klebsiella pneumoniae pantothenate kinase in complex with N-pentylpantothenamide
ComponentsPantothenate kinase
KeywordsTRANSFERASE / BIOSYNTHETIC PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / P-loop kinase
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-pentylpantothenamide / ADENOSINE-5'-DIPHOSPHATE / Chem-PN4 / Pantothenate kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 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
DepositionMay 16, 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)313,12363
Polymers307,6868
Non-polymers5,43655
Water17,781987
1
A: Pantothenate kinase
C: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,35314
Polymers76,9222
Non-polymers1,43112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-38 kcal/mol
Surface area25310 Å2
MethodPISA
2
B: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,35321
Polymers76,9222
Non-polymers1,43119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-39 kcal/mol
Surface area25290 Å2
MethodPISA
3
E: Pantothenate kinase
F: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,35313
Polymers76,9222
Non-polymers1,43111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-37 kcal/mol
Surface area25180 Å2
MethodPISA
4
G: Pantothenate kinase
H: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,06415
Polymers76,9222
Non-polymers1,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-36 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.837, 130.825, 192.150
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-PN4 / (2R)-2,4-dihydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide / N-Pentylpantothenamide


Type: peptide-like, Non-polymer / Class: Antibiotic, Antimicrobial / Mass: 288.383 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H28N2O4 / References: N-pentylpantothenamide
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 40 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.5 uL protein + 0.5 uL buffer (20% PEG3350, 0.2 M tri-lithium citrate) + 0.2 uL (+/-)-1,3-butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 187512 / Num. obs: 187511 / % possible obs: 99.95 % / Redundancy: 7.08 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.6649
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.1-2.216.680.918129427124199.91
2.21-2.356.820.6417536525722199.94
2.35-2.516.980.4816863324164199.95
2.51-2.717.120.3316056422559199.98
2.71-2.977.250.2115068420779199.97
2.97-3.327.360.1313890818861199.99
3.32-3.837.360.08123145167211100
3.83-4.77.270.0510318214196199.99
4.7-6.647.380.0581853110971100
6.64-406.990.04440206296199.45

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementResolution: 2.1→39.645 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / Matrix type: sparse / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.501 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 9425 5.031 %RANDOM
Rwork0.1852 177902 --
obs0.187 187327 99.879 %-
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: 107.33 Å2 / Biso mean: 27.292 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.826 Å20 Å2-0 Å2
2---0.723 Å20 Å2
3---1.549 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19893 0 396 987 21276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01920755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219880
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9828217
X-RAY DIFFRACTIONr_angle_other_deg0.7723.00145492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91352461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27823.727966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.618153563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26315143
X-RAY DIFFRACTIONr_chiral_restr0.0780.23155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024830
X-RAY DIFFRACTIONr_mcbond_it1.7242.6079841
X-RAY DIFFRACTIONr_mcbond_other1.7232.6079840
X-RAY DIFFRACTIONr_mcangle_it2.7983.90212288
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
2.1-2.1540.2937110.245130150.2481374399.8760.226
2.154-2.2130.2736760.232126310.2341333299.8120.21
2.213-2.2770.2636550.218123330.221300199.90.193
2.277-2.3470.2746530.208119920.2121266499.850.181
2.347-2.4240.266390.205116060.2081225699.910.177
2.424-2.5080.2486180.2112420.2021187499.8820.171
2.508-2.6030.2445860.195108540.1971144999.9210.165
2.603-2.7090.2445480.194104850.1961104299.9180.166
2.709-2.8280.245270.188100690.1911060799.8960.162
2.828-2.9660.2375050.1996260.1931014299.8920.166
2.966-3.1250.2244720.19192030.192967899.9690.171
3.125-3.3130.2414650.19686860.198915999.9130.179
3.313-3.540.2334140.18982280.191864499.9770.174
3.54-3.8220.2063820.17476700.176805599.9630.162
3.822-4.1820.173620.15270700.153743899.9190.143
4.182-4.670.1793400.13964190.141676899.8670.133
4.67-5.380.1812960.15157230.152602299.950.144
5.38-6.5580.2142500.18248790.184513299.9420.17
6.558-9.1510.1772010.15638600.157406399.9510.156
9.151-39.6450.2181250.1823100.182244499.6320.189

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