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- PDB-3ll3: The crystal structure of ligand bound xylulose kinase from Lactob... -

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Basic information

Entry
Database: PDB / ID: 3ll3
TitleThe crystal structure of ligand bound xylulose kinase from Lactobacillus acidophilus
ComponentsGluconate kinase
KeywordsTRANSFERASE / xylulose kinase / 11120e1 / NYSGX / ATP / ADP / xylulose / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


gluconokinase / gluconokinase activity / carbohydrate metabolic process / phosphorylation / ATP binding
Similarity search - Function
FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE / D-XYLULOSE / Gluconate kinase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of xylulose kinase from Lactobacillus acidophilus
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gluconate kinase
B: Gluconate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7727
Polymers112,2592
Non-polymers1,5135
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-37 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.889, 73.056, 82.872
Angle α, β, γ (deg.)84.75, 86.32, 77.95
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Gluconate kinase


Mass: 56129.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: LBA0354 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)codon+ril / References: UniProt: Q5FM28, gluconokinase
#4: Sugar ChemComp-XUL / D-XYLULOSE


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5

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Non-polymers , 4 types, 631 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-DXP / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE


Mass: 214.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O7P
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M HEPEs pH 7.5, 25% w/v Polyethylene glycol, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 79750 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 1.63 / Num. unique all: 8387 / % possible all: 77

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBT

3gbt


Resolution: 2.002→36.138 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 26.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3962 4.97 %Random
Rwork0.1956 ---
obs0.197 79750 89.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.711 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 27.18 Å2
Baniso -1Baniso -2Baniso -3
1--7.2008 Å2-1.929 Å2-4.553 Å2
2--5.7133 Å210.7448 Å2
3---1.4874 Å2
Refinement stepCycle: LAST / Resolution: 2.002→36.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7608 0 94 627 8329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087859
X-RAY DIFFRACTIONf_angle_d1.15210665
X-RAY DIFFRACTIONf_dihedral_angle_d18.8452921
X-RAY DIFFRACTIONf_chiral_restr0.0751201
X-RAY DIFFRACTIONf_plane_restr0.0061345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0019-2.02630.3429910.28391988X-RAY DIFFRACTION65
2.0263-2.0520.31381330.28392405X-RAY DIFFRACTION81
2.052-2.0790.34971270.26662535X-RAY DIFFRACTION83
2.079-2.10740.29631330.25742508X-RAY DIFFRACTION86
2.1074-2.13750.31280.24352569X-RAY DIFFRACTION83
2.1375-2.16940.24591210.23922561X-RAY DIFFRACTION85
2.1694-2.20330.28551200.23272564X-RAY DIFFRACTION84
2.2033-2.23950.24731270.24182499X-RAY DIFFRACTION82
2.2395-2.27810.27861240.26472576X-RAY DIFFRACTION86
2.2781-2.31950.26261260.23082549X-RAY DIFFRACTION83
2.3195-2.36410.28441480.21482596X-RAY DIFFRACTION87
2.3641-2.41230.25921410.20362642X-RAY DIFFRACTION87
2.4123-2.46480.25921310.20512694X-RAY DIFFRACTION89
2.4648-2.52210.25441390.21572766X-RAY DIFFRACTION90
2.5221-2.58520.26171490.22662708X-RAY DIFFRACTION92
2.5852-2.6550.26681440.22032827X-RAY DIFFRACTION93
2.655-2.73310.27091470.20922818X-RAY DIFFRACTION94
2.7331-2.82130.25291460.21042866X-RAY DIFFRACTION94
2.8213-2.92210.24121540.20962869X-RAY DIFFRACTION95
2.9221-3.0390.21921490.20662912X-RAY DIFFRACTION96
3.039-3.17730.26551460.21052919X-RAY DIFFRACTION97
3.1773-3.34470.23351640.19132896X-RAY DIFFRACTION97
3.3447-3.55410.221840.18352908X-RAY DIFFRACTION97
3.5541-3.82820.20341530.17042949X-RAY DIFFRACTION97
3.8282-4.21290.17971580.15582839X-RAY DIFFRACTION95
4.2129-4.82130.15621640.13583001X-RAY DIFFRACTION98
4.8213-6.06970.16011590.15472987X-RAY DIFFRACTION99
6.0697-36.14410.18241560.17892837X-RAY DIFFRACTION94

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