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- PDB-5b8h: Crystal Structure of Type III pantothenate kinase (PanK III) from... -

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Basic information

Entry
Database: PDB / ID: 5b8h
TitleCrystal Structure of Type III pantothenate kinase (PanK III) from Burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP
ComponentsType III pantothenate kinase
KeywordsTRANSFERASE / SSGCID / Type III pantothenate kinase / Burkholderia cenocepacia / coaX / CoA biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
IMIDODIPHOSPHORIC ACID / ADENOSINE MONOPHOSPHATE / PANTOTHENOIC ACID / Type III pantothenate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1999 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Type III pantothenate kinase (PanK III) from Burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP
Authors: SSGCID / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,7569
Polymers61,4922
Non-polymers1,2647
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-14 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.210, 72.750, 154.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 30745.955 Da / Num. of mol.: 2 / Fragment: BuceA.17924.a.ER1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: coaX, BceJ2315_06870, BCAL0693 / Plasmid: BuceA.17924.a.ER1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E9P3, pantothenate kinase

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5NO6P2
#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.: 2 / Source method: obtained synthetically / Formula: C9H17NO5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BuceA.17924.a.ER1.PD00352 at 10.1 mg/ml incubated with 3 mM MgCl2, pantothenate, AMPPNP, then mixed 1:1 with MCSG2(a11): 20% PEG-3350, 0.2 M Lithium Chloride, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1999→50 Å / Num. obs: 25825 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.53 Å2 / Rmerge F obs: 0.986 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.165 / Χ2: 0.94 / Net I/σ(I): 8.69 / Num. measured all: 85516
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.263.30.6610.5492.546275187818710.65799.6
2.26-2.320.7290.4632.866127184718390.55599.6
2.32-2.390.8130.423.235926178417770.50399.6
2.39-2.460.8250.3693.575852176017500.44299.4
2.46-2.540.8320.3344.035581167916700.40199.5
2.54-2.630.8850.2994.365486165916490.35899.4
2.63-2.730.9070.2475.235268158415790.29699.7
2.73-2.840.9290.2175.985101153915320.2699.5
2.84-2.970.950.1787.084904147514660.21399.4
2.97-3.110.9570.1568.064606139413870.18799.5
3.11-3.280.9850.1189.744481136313550.14199.4
3.28-3.480.9850.111.554200127612570.11998.5
3.48-3.720.990.08113.983954120711950.09699
3.72-4.020.9920.06715.853684113111150.0898.6
4.02-4.40.9940.05519.023372104110200.06598
4.4-4.920.9960.0519.8530899649400.0697.5
4.92-5.680.9950.05418.3526688478260.06497.5
5.68-6.960.9950.05816.9722397206980.0796.9
6.96-9.840.9980.03923.8717785875640.04796.1
9.84-500.9980.03226.379253703350.03990.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.66 Å44.21 Å
Translation4.66 Å44.21 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O5F

2o5f


Resolution: 2.1999→19.698 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1307 5.08 %
Rwork0.1878 24433 -
obs0.1899 25740 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.67 Å2 / Biso mean: 23.6565 Å2 / Biso min: 3.47 Å2
Refinement stepCycle: final / Resolution: 2.1999→19.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 79 222 4003
Biso mean--38.11 24.86 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023898
X-RAY DIFFRACTIONf_angle_d0.6655348
X-RAY DIFFRACTIONf_chiral_restr0.027618
X-RAY DIFFRACTIONf_plane_restr0.002687
X-RAY DIFFRACTIONf_dihedral_angle_d10.5981334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1999-2.28780.28751430.241426672810100
2.2878-2.39180.28541400.230226732813100
2.3918-2.51760.25231390.224927042843100
2.5176-2.6750.30581350.221127032838100
2.675-2.8810.24981530.21326812834100
2.881-3.16980.24211400.1932749288999
3.1698-3.6260.20521330.17742724285799
3.626-4.5590.19021530.14572726287998
4.559-19.69890.18521710.15822806297797
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)
12.06560.4251.21152.65460.5011.7181-0.30320.09140.5053-0.12890.0127-0.008-0.40850.09530.10850.1738-0.04-0.02350.1909-0.0650.301918.338432.015936.3843
20.9147-0.05470.06220.47930.13440.6457-0.02720.01750.0141-0.01290.00220.02220.03080.050.02310.0718-0.00720.00170.0916-0.00140.08636.97218.623130.165
32.1297-0.88371.14441.10580.39744.20020.0360.07890.4224-0.238-0.0516-0.0707-0.41070.04710.02450.14230.03380.03620.09770.01620.2062-4.179124.077130.1425
46.50260.23531.80935.43831.7651.5472-0.2306-0.63560.22690.3543-0.05660.1023-0.0126-0.54190.23780.10980.02990.01480.1751-0.030.194210.973726.02245.0279
56.01583.98570.90566.24540.67011.6642-0.06320.2312-0.45970.0525-0.35130.57350.4994-0.55840.3640.28970.01720.04530.3418-0.12850.39063.374-6.1415-3.0476
63.4639-0.5157-0.12171.45910.81865.3055-0.0370.0811-0.7636-0.18620.1533-0.31440.78120.3328-0.15980.36380.01630.04160.2425-0.04730.371211.5184-9.3216-1.3466
70.32050.4610.16590.9945-0.30630.99740.09940.321-0.3323-0.3545-0.1065-0.22210.13850.136-0.020.25260.05330.06940.2671-0.08970.193210.4732-0.4421-8.4645
81.57330.17341.50611.22830.35552.8026-0.00240.1516-0.0498-0.2231-0.02430.09130.1045-0.06730.01210.11830.01280.00260.1812-0.03230.1077-3.61428.38335.4112
91.05970.63730.24783.59260.57052.70060.08620.1465-0.4441-0.0663-0.0569-0.12570.1877-0.3045-0.0860.12050.0345-0.02730.12880.02950.21327.40782.299529.3036
103.3205-1.07772.45960.8409-0.83724.5379-0.15710.027-0.09620.00960.02950.0964-0.0923-0.41850.08730.1324-0.05440.03430.13770.01780.1391-5.54599.049920.6915
112.4982-0.247-1.00490.70851.46243.13710.16270.1778-0.24670.0511-0.0284-0.08910.3634-0.455-0.15730.1815-0.0418-0.03580.15380.00250.2171-7.453-0.28319.0639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 51 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 245 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 257 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 25 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 51 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 87 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 161 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 188 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 189 through 216 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 217 through 257 )B0

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