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- PDB-4e8z: Crystal Structure of Burkholderia cenocepacia HldA in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 4e8z
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


heptose 7-phosphate kinase activity / heptose-1-phosphate adenylyltransferase activity / phosphotransferase activity, alcohol group as acceptor / cytosol
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-IHC / : / D-beta-D-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 1.3Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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: D-beta-D-heptose 7-phosphate kinase
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7426
Polymers76,7392
Non-polymers1,0034
Water1,964109
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)77,7426
Polymers76,7392
Non-polymers1,0034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area2620 Å2
ΔGint-10 kcal/mol
Surface area26210 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)77,7426
Polymers76,7392
Non-polymers1,0034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area2690 Å2
ΔGint-9 kcal/mol
Surface area26120 Å2
MethodPISA
3
A: D-beta-D-heptose 7-phosphate kinase
B: D-beta-D-heptose 7-phosphate kinase
hetero molecules

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)155,48512
Polymers153,4794
Non-polymers2,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area7860 Å2
ΔGint-24 kcal/mol
Surface area49770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.766, 68.766, 338.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-632-

HOH

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Components

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


Mass: 462.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13Cl2N5O3S
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 2% PEG 400, 2.0M ammonium sulfate, 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: 3.05→48.63 Å / Num. all: 16447 / Num. obs: 16447 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.05→3.1 Å / % possible all: 93.1

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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: 3.05→48.63 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 25.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 826 5.05 %RANDOM
Rwork0.2168 ---
obs0.2197 16368 --
all-16447 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.11 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3723 Å20 Å2-0 Å2
2--4.3723 Å2-0 Å2
3----8.7446 Å2
Refinement stepCycle: LAST / Resolution: 3.05→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 62 109 4819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084795
X-RAY DIFFRACTIONf_angle_d0.8126515
X-RAY DIFFRACTIONf_dihedral_angle_d15.0331750
X-RAY DIFFRACTIONf_chiral_restr0.044769
X-RAY DIFFRACTIONf_plane_restr0.004852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.23840.37081480.30522382X-RAY DIFFRACTION95
3.2384-3.48840.31671400.25032539X-RAY DIFFRACTION99
3.4884-3.83930.28071460.21612542X-RAY DIFFRACTION99
3.8393-4.39450.23541240.18492585X-RAY DIFFRACTION100
4.3945-5.53540.24971260.18232648X-RAY DIFFRACTION100
5.5354-48.63110.27611420.23232846X-RAY DIFFRACTION100
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)
10.946-0.76511.56923.6724-2.68295.3830.40890.2828-0.3272-0.6953-0.4521-0.37180.88881.05380.13650.52070.08690.1370.64870.02670.5958-23.3672-7.267811.0229
20.4595-1.27190.34963.9204-3.46695.723-0.2256-0.1145-0.1732-0.0245-0.0824-0.0940.53410.27830.34760.60920.040.10920.53490.05380.5342-27.7842-10.980810.9976
32.84592.36431.18513.28830.61645.46850.1851-0.20470.64840.3456-0.59840.2053-0.32660.09470.44790.5448-0.0920.10910.50340.04230.7004-31.1898-9.449530.4479
40.00010.0011-0.0013-0.00130.0012-0.0031-0.02390.6778-0.4639-0.61170.7867-0.3815-0.57410.8311-0.72771.6339-0.6420.04611.1227-0.34082.7852-24.496215.253734.6383
55.19183.39481.6085.5654-2.3333.90920.0846-0.68450.76250.2453-0.9724-0.3769-1.40241.30510.72481.0787-0.3791-0.07761.16880.01470.9554-17.6454.327433.8897
63.67420.5602-2.60255.2873-2.37054.87760.2329-0.27990.5977-0.4051-0.707-1.1472-0.22051.9540.51350.7404-0.25570.10071.11750.12341.0025-11.7297-7.554125.1768
72.0714-1.2392-1.37511.96780.26692.70610.20390.54570.1194-0.1686-0.18330.1915-0.1296-0.6609-0.05290.6264-0.0174-0.09660.59920.02260.5849-48.7435-40.21864.0124
82.0198-3.01551.91422.0138-3.73148.93380.13880.05420.6646-1.697-0.2571-0.24620.6399-1.14850.19940.7887-0.06250.0230.670.01150.7478-56.6568-34.265511.1356
91.0991-1.0839-2.14866.2122.84096.2604-0.1719-0.07240.1947-0.13520.28980.0674-0.93010.5703-0.08610.67930.0535-0.0430.5427-0.01250.4813-41.832-36.14389.346
104.99851.3789-0.85722.2874-1.1332.82280.2582-0.3541-0.53070.0837-0.18070.30350.63370.0513-0.10570.9888-0.1199-0.06540.5537-0.07640.6924-54.2283-42.450128.3369
116.3348-2.16181.32514.0707-0.1630.31.0967-0.1435-0.7830.5512-0.70470.53350.01160.5456-0.3351.3999-0.8011-0.15861.2615-0.13711.1482-68.495-49.780520.5061
124.58071.22171.86065.32321.74047.80840.70230.9179-0.6218-0.8513-0.310.4170.988-1.5809-0.39270.9095-0.1502-0.23951.0827-0.0640.7519-65.964-39.856913.6122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:48)
2X-RAY DIFFRACTION2(chain A and resid 49:131)
3X-RAY DIFFRACTION3(chain A and resid 132:209)
4X-RAY DIFFRACTION4(chain A and resid 210:215)
5X-RAY DIFFRACTION5(chain A and resid 216:265)
6X-RAY DIFFRACTION6(chain A and resid 266:314)
7X-RAY DIFFRACTION7(chain B and resid 6:55)
8X-RAY DIFFRACTION8(chain B and resid 56:73)
9X-RAY DIFFRACTION9(chain B and resid 74:134)
10X-RAY DIFFRACTION10(chain B and resid 135:242)
11X-RAY DIFFRACTION11(chain B and resid 243:263)
12X-RAY DIFFRACTION12(chain B and resid 264:316)

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