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- PDB-4e84: Crystal Structure of Burkholderia cenocepacia HldA -

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Basic information

Entry
Database: PDB / ID: 4.0E+84
TitleCrystal Structure of Burkholderia cenocepacia HldA
ComponentsD-beta-D-heptose 7-phosphate kinase
KeywordsTRANSFERASE / LPS-heptose Biosynthesis / Beta-clasp dimerization region / PfkB Carbohydrate Kinase / Phosphorylation
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-GMZ / : / Chem-M7B / PHOSPHATE ION / D-beta-D-heptose 7-phosphate kinase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLee, T.-W. / 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 19, 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_atom_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)79,55014
Polymers77,4902
Non-polymers2,06012
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-66 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.398, 90.398, 397.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

21B-688-

HOH

31B-689-

HOH

41B-746-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38744.902 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

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-M7B / 7-O-phosphono-D-glycero-beta-D-manno-heptopyranose


Type: D-saccharide, beta linking / Mass: 290.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O10P
#8: Sugar ChemComp-GMZ / 1,7-di-O-phosphono-D-glycero-beta-D-manno-heptopyranose


Type: D-saccharide / Mass: 370.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O13P2

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Non-polymers , 6 types, 335 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#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


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium citrate, 0.1M HEPES, 20% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→38.96 Å / Num. all: 31023 / Num. obs: 31023 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.6→38.955 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 1552 5.06 %
Rwork0.2244 --
obs0.2264 30655 99.1 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.583 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4246 Å20 Å20 Å2
2--0.4246 Å20 Å2
3----0.8491 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 110 325 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064921
X-RAY DIFFRACTIONf_angle_d0.6956697
X-RAY DIFFRACTIONf_dihedral_angle_d21.3151905
X-RAY DIFFRACTIONf_chiral_restr0.04799
X-RAY DIFFRACTIONf_plane_restr0.003861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68240.47321450.41722489X-RAY DIFFRACTION97
2.6824-2.77830.40091240.34742536X-RAY DIFFRACTION98
2.7783-2.88950.3581300.272612X-RAY DIFFRACTION100
2.8895-3.0210.3181260.24762647X-RAY DIFFRACTION100
3.021-3.18020.27531550.22482573X-RAY DIFFRACTION100
3.1802-3.37930.27981320.23092627X-RAY DIFFRACTION99
3.3793-3.640.28061580.25022571X-RAY DIFFRACTION97
3.64-4.0060.27611490.24122619X-RAY DIFFRACTION99
4.006-4.58490.20771480.17712711X-RAY DIFFRACTION100
4.5849-5.77350.21771400.18092744X-RAY DIFFRACTION100
5.7735-38.95980.21651450.20162974X-RAY DIFFRACTION100

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