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- PDB-4e8y: Crystal Structure of Burkholderia cenocepacia HldA in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 4e8y
TitleCrystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor
ComponentsD-beta-D-heptose 7-phosphate kinase
KeywordsTransferase/Transferase Inhibitor / LPS-heptose Biosynthesis / Beta-clasp Dimerization Region / PfkB Carbohydrate Kinase / Phosphorylation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / nucleotidyltransferase activity / kinase activity / carbohydrate metabolic process / phosphorylation
Similarity search - Function
RfaE bifunctional protein, domain I / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IHA / : / Chem-M7B / PHOSPHATE ION / D-beta-D-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, T.-W. / Verhey, T.B. / Junop, M.S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural-functional studies of Burkholderia cenocepacia D-glycero-beta-D-manno-heptose 7-phosphate kinase (HldA) and characterization of inhibitors with antibiotic adjuvant and antivirulence properties.
Authors: Lee, T.W. / Verhey, T.B. / Antiperovitch, P.A. / Atamanyuk, D. / Desroy, N. / Oliveira, C. / Denis, A. / Gerusz, V. / Drocourt, E. / Loutet, S.A. / Hamad, M.A. / Stanetty, C. / Andres, S.N. ...Authors: Lee, T.W. / Verhey, T.B. / Antiperovitch, P.A. / Atamanyuk, D. / Desroy, N. / Oliveira, C. / Denis, A. / Gerusz, V. / Drocourt, E. / Loutet, S.A. / Hamad, M.A. / Stanetty, C. / Andres, S.N. / Sugiman-Marangos, S. / Kosma, P. / Valvano, M.A. / Moreau, F. / Junop, M.S.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-beta-D-heptose 7-phosphate kinase
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,18110
Polymers76,7392
Non-polymers1,4418
Water5,332296
1
A: D-beta-D-heptose 7-phosphate kinase
hetero molecules

A: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,37610
Polymers76,7392
Non-polymers1,6368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3000 Å2
ΔGint-31 kcal/mol
Surface area25300 Å2
MethodPISA
2
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules

B: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98510
Polymers76,7392
Non-polymers1,2468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3460 Å2
ΔGint-43 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.563, 69.200, 92.518
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-742-

HOH

21B-618-

HOH

31B-680-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein D-beta-D-heptose 7-phosphate kinase


Mass: 38369.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: hldA, BceJ2315_28810, BCAL2945 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EB35
#3: Sugar ChemComp-M7B / 7-O-phosphono-D-glycero-beta-D-manno-heptopyranose / 7-O-phosphono-D-glycero-beta-D-manno-heptose / 7-O-phosphono-D-glycero-D-manno-heptose / 7-O-phosphono-D-glycero-manno-heptose


Type: D-saccharide, beta linking / Mass: 290.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O10P

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Non-polymers , 5 types, 303 molecules

#2: Chemical ChemComp-IHA / {[2-({[5-(2,6-dimethoxyphenyl)-1,2,4-triazin-3-yl]amino}methyl)-1,3-benzothiazol-5-yl]oxy}acetic acid


Mass: 453.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N5O5S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20% PEG 10000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.59→45.35 Å / Num. all: 20632 / Num. obs: 20632 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.59→2.64 Å / % possible all: 85.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E84

4e84


Resolution: 2.6→45.35 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1055 5.11 %RANDOM
Rwork0.1901 ---
obs0.1925 20626 --
all-20626 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.174 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8203 Å20 Å2-1.9478 Å2
2---4.586 Å2-0 Å2
3---2.7657 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 91 296 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014840
X-RAY DIFFRACTIONf_angle_d0.8566582
X-RAY DIFFRACTIONf_dihedral_angle_d18.3871801
X-RAY DIFFRACTIONf_chiral_restr0.047775
X-RAY DIFFRACTIONf_plane_restr0.004858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70560.32651390.25562345X-RAY DIFFRACTION83
2.7056-2.84820.25551200.22592513X-RAY DIFFRACTION88
2.8482-3.02660.30011280.22282527X-RAY DIFFRACTION88
3.0266-3.26030.28651400.21282461X-RAY DIFFRACTION87
3.2603-3.58820.25271210.18452481X-RAY DIFFRACTION87
3.5882-4.10720.18331330.16072446X-RAY DIFFRACTION85
4.1072-5.17340.20481490.14652417X-RAY DIFFRACTION85
5.1734-45.35990.22611250.20862381X-RAY DIFFRACTION81
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)
10.57250.3756-1.31141.5762-0.99992.71590.1146-0.1937-0.13460.0985-0.2678-0.4464-0.17340.47860.11660.22020.03-0.04660.36190.01240.35542.2194-0.156341.5155
21.36260.34-0.04452.3774-1.27881.09410.14120.1560.2383-0.0658-0.0250.0757-0.1228-0.0193-0.10490.26190.07740.01090.2404-0.02880.26050.38656.252128.5584
32.3842-0.1622-0.07772.66870.75652.08130.07250.1481-0.1656-0.2465-0.0898-0.14210.24360.13880.01230.36020.16320.01580.3799-0.01470.352713.5081-8.512922.6559
42.0007-1.64395.38442.00162.79762.00160.1199-0.25421.67320.336-0.6634-0.671-1.10120.14650.56340.80570.0314-0.03380.53130.0560.585221.23942.69937.7896
50.3323-0.26120.28372.3475-1.83673.67150.05170.0383-0.097-0.125-0.1151-0.13520.35550.14830.06020.19420.00660.01290.1848-0.04790.2437-5.30630.148558.0156
65.0508-1.24140.49323.3845-0.27083.55210.2009-0.4728-0.4260.3126-0.24160.09780.2307-0.19670.02590.2835-0.0721-0.01090.24130.01190.289-7.966229.403976.5941
74.01780.9574-1.33116.22440.30753.7662-0.0762-0.32461.03530.20290.01410.7092-0.7408-0.22690.08420.36280.0131-0.06480.2793-0.07750.4457-4.404245.706880.8536
82.39760.4204-0.4332.3711-0.19193.187-0.01560.20.0284-0.14650.0484-0.5350.02430.3471-0.03250.2712-0.0271-0.02760.31040.03040.320710.427938.135472.3814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:56 )A7 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:179 )A57 - 179
3X-RAY DIFFRACTION3( CHAIN A AND RESID 180:307 )A180 - 307
4X-RAY DIFFRACTION4( CHAIN A AND RESID 308:314 )A308 - 314
5X-RAY DIFFRACTION5( CHAIN B AND RESID 9:149 )B9 - 149
6X-RAY DIFFRACTION6( CHAIN B AND RESID 150:187 )B150 - 187
7X-RAY DIFFRACTION7( CHAIN B AND RESID 188:239 )B188 - 239
8X-RAY DIFFRACTION8( CHAIN B AND RESID 240:315 )B240 - 315

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