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- PDB-1sq5: Crystal Structure of E. coli Pantothenate kinase -

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Basic information

Entry
Database: PDB / ID: 1sq5
TitleCrystal Structure of E. coli Pantothenate kinase
ComponentsPantothenate kinase
KeywordsTRANSFERASE / P-loop
Function / homology
Function and homology information


pantetheine kinase activity / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / protein homodimerization activity / 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
ADENOSINE-5'-DIPHOSPHATE / PANTOTHENOIC ACID / Pantothenate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIvey, R.A. / Zhang, Y.-M. / Virga, K.G. / Hevener, K. / Lee, R.E. / Rock, C.O. / Jackowski, S. / Park, H.-W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The structure of the pantothenate kinase.ADP.pantothenate ternary complex reveals the relationship between the binding sites for substrate, allosteric regulator, and antimetabolites.
Authors: Ivey, R.A. / Zhang, Y.-M. / Virga, K.G. / Hevener, K. / Lee, R.E. / Rock, C.O. / Jackowski, S. / Park, H.-W.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Pantothenate kinase
C: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,48012
Polymers141,8944
Non-polymers2,5868
Water15,943885
1
A: Pantothenate kinase
D: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2406
Polymers70,9472
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-39 kcal/mol
Surface area25950 Å2
MethodPISA
2
B: Pantothenate kinase
hetero molecules

B: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2406
Polymers70,9472
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
3
C: Pantothenate kinase
hetero molecules

C: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2406
Polymers70,9472
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)181.203, 181.655, 47.418
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pantothenate kinase / Pantothenic acid kinase / Rts protein


Mass: 35473.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COAA, RTS, PANK, B3974, C4933, Z5545, ECS4901 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6I3, pantothenate kinase
#2: Chemical
ChemComp-PAU / PANTOTHENOIC ACID / N-[(2R)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANOYL]-BETA-ALANINE


Type: peptide-like / Mass: 219.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO5
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 70252 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.069 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.034 / % possible all: 98.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cross valid method: MOLEMAN2 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.187 --
obs0.187 65592 99.2 %
Displacement parametersBiso mean: 29.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati sigma a0.43 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9650 0 168 885 10703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.21 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.243 87
Rwork0.212 776

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