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- PDB-4o5f: Crystal structure of Type III pantothenate kinase from Burkholder... -

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Basic information

Entry
Database: PDB / ID: 4o5f
TitleCrystal structure of Type III pantothenate kinase from Burkholderia thailandensis in complex with pantothenate and phosphate
ComponentsType III pantothenate kinase
KeywordsTRANSFERASE / SSGCID / Type III pantothenate kinase / Pantothenate / kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / pantothenate kinase / phosphate
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP 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'-TRIPHOSPHATE / : / PANTOTHENOIC ACID / PHOSPHATE ION / Type III pantothenate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis in complex with pantothenate and phosphate
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D. / Fairman, J.W. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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

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Assembly

Deposited unit
A: Type III pantothenate kinase
B: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71715
Polymers58,6492
Non-polymers2,06813
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-40 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.440, 99.440, 112.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-453-

HOH

31A-482-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29324.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0369, coaX / Plasmid: ButhA.17294.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T1M2, pantothenate kinase

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Non-polymers , 7 types, 524 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C9H17NO5
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Rigaku Reagents, Wizard 3/4 c8 : 40mM KH2PO4, 16% PEG 8000, 20 % glycerol; ButhA.17924.a.A1.PS01175 at 18.1mg/ml, 5mM pantothenate, 5mM ATP, 5mM MgCl2, tray 250051c8, puck jqa3-7, direct ...Details: Rigaku Reagents, Wizard 3/4 c8 : 40mM KH2PO4, 16% PEG 8000, 20 % glycerol; ButhA.17924.a.A1.PS01175 at 18.1mg/ml, 5mM pantothenate, 5mM ATP, 5mM MgCl2, tray 250051c8, puck jqa3-7, direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 82475 / Num. obs: 82347 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 26.493 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.590.5753.82588965990199.9
1.59-1.630.4584.795809558941100
1.63-1.680.3526.175620456861100
1.68-1.730.2957.445490255541100
1.73-1.790.2279.545326853701100
1.79-1.850.17711.915162652071100
1.85-1.920.13415.824991750271100
1.92-20.10919.274831848521100
2-2.090.08723.954641746701100
2.09-2.190.06929.614408444461100
2.19-2.310.06133.84237442901100
2.31-2.450.0539.483963740071100
2.45-2.620.04643.36374263809199.9
2.62-2.830.0448.583483335621100
2.83-3.10.03654.063175832771100
3.1-3.470.0361.64287002983199.8
3.47-40.02766.43251892647199.6
4-4.90.02568.17212122272199.6
4.9-6.930.02467.23166681806199.7
6.93-500.02363.697679998192

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2f9t, modified with CCP4 program chainsaw, search with two domains

2f9t


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.348 / SU ML: 0.044 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4176 5.1 %RANDOM
Rwork0.1562 ---
all0.1575 82475 --
obs0.1575 82268 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.7 Å2 / Biso mean: 27.1303 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 88 511 4281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194052
X-RAY DIFFRACTIONr_bond_other_d0.0020.023879
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9615597
X-RAY DIFFRACTIONr_angle_other_deg0.8438893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05221.837147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214642
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02936
X-RAY DIFFRACTIONr_mcbond_it0.9681.2192092
X-RAY DIFFRACTIONr_mcbond_other0.9681.2192093
X-RAY DIFFRACTIONr_mcangle_it1.6261.8222624
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 296 -
Rwork0.198 5683 -
all-5979 -
obs-5990 99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.69131.58022.1792.31781.56074.35860.1489-0.7624-0.74540.44320.0369-0.26560.77110.1629-0.18580.24240.092-0.01390.26370.08870.09114.82124.45633.302
20.4867-0.1276-0.11740.83310.50170.59710.0279-0.06270.01280.0023-0.0077-0.01630.00710.0137-0.02020.09190.00260.0170.1156-0.00610.00421.37528.44613.175
36.60370.40453.49622.10070.27677.29780.0292-0.2805-0.4726-0.01360.12270.18110.2437-1.5458-0.15190.0817-0.11140.03340.5791-0.05270.1106-27.5154.206-8.999
40.65940.1033-0.08321.04161.04291.52960.0090.1096-0.0018-0.1376-0.09440.105-0.1288-0.18660.08540.09270.0178-0.0060.1521-0.02350.0153-9.59618.218-6.305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 69
2X-RAY DIFFRACTION2A70 - 301
3X-RAY DIFFRACTION3B4 - 77
4X-RAY DIFFRACTION4B78 - 302

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