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- PDB-3bex: Type III pantothenate kinase from Thermotoga maritima complexed w... -

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Basic information

Entry
Database: PDB / ID: 3bex
TitleType III pantothenate kinase from Thermotoga maritima complexed with pantothenate
ComponentsType III pantothenate kinase
KeywordsTRANSFERASE / Actin-like fold / ATP-binding / Coenzyme A biosynthesis / Cytoplasm / Kinase / Metal-binding / Nucleotide-binding / Potassium
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PANTOTHENOIC ACID / PHOSPHATE ION / Type III pantothenate kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsYang, K. / Huerta, C. / Strauss, E. / Zhang, H.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis for substrate binding and the catalytic mechanism of type III pantothenate kinase.
Authors: Yang, K. / Strauss, E. / Huerta, C. / Zhang, H.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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: Type III pantothenate kinase
B: Type III pantothenate kinase
C: Type III pantothenate kinase
D: Type III pantothenate kinase
E: Type III pantothenate kinase
F: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,07018
Polymers165,1846
Non-polymers1,88512
Water32,5531807
1
A: Type III pantothenate kinase
B: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6906
Polymers55,0612
Non-polymers6284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
MethodPISA
2
C: Type III pantothenate kinase
D: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6906
Polymers55,0612
Non-polymers6284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
MethodPISA
3
E: Type III pantothenate kinase
F: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6906
Polymers55,0612
Non-polymers6284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.917, 136.991, 74.970
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27530.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: coaX / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZY5, pantothenate kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: 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.: 6 / Source method: obtained synthetically / Formula: C9H17NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1807 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 2250, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 209057 / % possible obs: 99.7 % / Rsym value: 0.061 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GTD

2gtd


Resolution: 1.51→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.37 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21345 11057 5 %RANDOM
Rwork0.18442 ---
obs0.18589 209057 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20.07 Å2
2--0.54 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11574 0 120 1807 13501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211934
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.96116158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3351482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95424.096498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.684152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6111554
X-RAY DIFFRACTIONr_chiral_restr0.2110.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.26103
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28316
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21646
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.292
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8411.57543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41211934
X-RAY DIFFRACTIONr_scbond_it2.20634925
X-RAY DIFFRACTIONr_scangle_it3.5674.54224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 764 -
Rwork0.28 14407 -
obs--94.16 %

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