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- PDB-4e8w: Crystal Structure of Burkholderia cenocepacia HldA in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 4e8w
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-IHA / : / D-beta-D-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8654 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_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_label_asym_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)77,7256
Polymers76,7392
Non-polymers9854
Water2,414134
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)77,7256
Polymers76,7392
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2640 Å2
ΔGint-7 kcal/mol
Surface area25080 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)77,7256
Polymers76,7392
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2670 Å2
ΔGint-6 kcal/mol
Surface area25230 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)155,44912
Polymers153,4794
Non-polymers1,9708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area7800 Å2
ΔGint-24 kcal/mol
Surface area47820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.579, 69.579, 336.445
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
11A-627-

HOH

21A-645-

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-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
#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.: 134 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
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: 2.85→49.2 Å / Num. all: 18187 / Num. obs: 18187 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.85→2.9 Å / % possible all: 93.3

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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: 2.8654→49.2 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 928 5.1 %RANDOM
Rwork0.2186 ---
obs0.2205 18181 --
all-18181 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.157 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6122 Å20 Å2-0 Å2
2--5.6122 Å2-0 Å2
3----11.2245 Å2
Refinement stepCycle: LAST / Resolution: 2.8654→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 66 134 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084736
X-RAY DIFFRACTIONf_angle_d0.8756442
X-RAY DIFFRACTIONf_dihedral_angle_d14.6131762
X-RAY DIFFRACTIONf_chiral_restr0.048757
X-RAY DIFFRACTIONf_plane_restr0.003841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8654-3.01650.31921240.27892389X-RAY DIFFRACTION90
3.0165-3.20540.29341570.25682432X-RAY DIFFRACTION93
3.2054-3.45290.31611400.22592446X-RAY DIFFRACTION92
3.4529-3.80020.2851360.212461X-RAY DIFFRACTION92
3.8002-4.34990.22221280.19262471X-RAY DIFFRACTION91
4.3499-5.47920.22681230.18062475X-RAY DIFFRACTION89
5.4792-49.2070.24421200.24612579X-RAY DIFFRACTION86
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)
10.0562-0.41660.20912.8744-2.92175.88010.03960.02350.18570.2926-0.2874-0.3505-0.570.540.22230.4621-0.0425-0.0420.35640.02740.47445.9095-24.7273-14.092
24.5706-1.22890.74454.80960.15454.70940.00830.5884-1.2587-0.0173-0.3572-0.20281.29820.63130.33950.7670.26640.1280.608-0.04030.6999.0203-36.0512-35.6118
35.091-2.01234.22196.19620.01624.0286-0.640.112-0.65190.43030.1502-0.38540.62241.78110.54620.57330.19720.18630.80580.22750.807619.4702-27.4545-29.5875
42.2433-0.70213.12484.3448-2.13074.67150.2625-0.9941-0.0270.5529-0.2499-0.6177-0.13570.2725-0.03480.65680.2657-0.16961.51980.35681.021524.1845-30.602-21.7694
51.42691.72770.80332.09090.97180.4518-0.1579-0.96340.58371.04320.1797-1.1247-0.35270.146-0.01470.73720.1407-0.14661.58680.16540.910529.8382-23.1917-23.3283
61.33320.93692.08772.29492.25673.81570.2032-0.1985-0.28520.2919-0.180.18990.4869-0.2181-0.03570.6465-0.00710.10690.35240.02420.4565-12.19570.9202-10.619
75.8173-0.53460.23685.5385-1.66066.13330.3350.33140.60710.1304-0.4397-0.0337-0.56120.03450.15030.64490.1380.01820.4804-0.05690.4557-20.30110.1618-28.134
82.35020.43930.29192.15560.27341.9605-0.0041-0.2030.50560.53410.02070.783-1.3068-1.1605-0.01031.01690.34120.14820.7087-0.07550.6311-30.729511.1626-23.3432
94.47632.75051.7353.8513-0.89472.534-0.8327-0.7895-0.7262-0.51270.3462-0.4063-0.1283-0.79810.48172.2807-0.16680.43431.2903-0.06360.8936-27.26446.0164-4.7944
100.6572-0.76530.61251.10290.0743.51680.2252-0.6713-0.07741.6262-0.01220.0333-0.0151-0.6066-0.211.7872-0.04950.12071.45780.00980.8406-37.3372-0.0329-7.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:165)
2X-RAY DIFFRACTION2(chain A and resid 166:258)
3X-RAY DIFFRACTION3(chain A and resid 259:290)
4X-RAY DIFFRACTION4(chain A and resid 291:310)
5X-RAY DIFFRACTION5(chain A and resid 311:315)
6X-RAY DIFFRACTION6(chain B and resid 7:170)
7X-RAY DIFFRACTION7(chain B and resid 171:214)
8X-RAY DIFFRACTION8(chain B and resid 215:300)
9X-RAY DIFFRACTION9(chain B and resid 301:310)
10X-RAY DIFFRACTION10(chain B and resid 311:315)

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