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- PDB-3bf1: Type III pantothenate kinase from Thermotoga maritima complexed w... -

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Basic information

Entry
Database: PDB / ID: 3bf1
TitleType III pantothenate kinase from Thermotoga maritima complexed with pantothenate and ADP
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
ADENOSINE-5'-DIPHOSPHATE / PANTOTHENOIC ACID / Type III pantothenate kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Feb 21, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)169,06318
Polymers165,1846
Non-polymers3,87912
Water11,674648
1
A: Type III pantothenate kinase
B: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3546
Polymers55,0612
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
MethodPISA
2
C: Type III pantothenate kinase
D: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3546
Polymers55,0612
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
MethodPISA
3
E: Type III pantothenate kinase
F: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3546
Polymers55,0612
Non-polymers1,2934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.962, 136.685, 75.010
Angle α, β, γ (deg.)90.00, 109.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: -2 - 245 / Label seq-ID: 1 - 248

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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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: pPro-EX / Production host: Escherichia coli (E. coli) / Strain (production host): BL20(DE3) / References: UniProt: Q9WZY5, pantothenate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 648 / 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: 43.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58933 / % possible obs: 98.9 % / Rsym value: 0.066

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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 / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.424 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.526 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25696 3156 5.1 %RANDOM
Rwork0.19027 ---
obs0.19363 58933 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.19 Å2
2---0.2 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11574 0 252 648 12474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.97616392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39851482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40424.096498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.339152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0461554
X-RAY DIFFRACTIONr_chiral_restr0.1590.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028922
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.25576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28196
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2811
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4971.57573
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.853211934
X-RAY DIFFRACTIONr_scbond_it1.14135138
X-RAY DIFFRACTIONr_scangle_it1.9734.54458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1929 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.420.5
2Bmedium positional0.430.5
3Cmedium positional0.370.5
4Dmedium positional0.450.5
5Emedium positional0.540.5
6Fmedium positional0.460.5
1Amedium thermal0.342
2Bmedium thermal0.472
3Cmedium thermal0.392
4Dmedium thermal0.332
5Emedium thermal0.382
6Fmedium thermal0.492
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 216 -
Rwork0.208 4164 -
obs--94.15 %

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