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- PDB-4c23: L-fuculose kinase -

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Basic information

Entry
Database: PDB / ID: 4c23
TitleL-fuculose kinase
ComponentsL-FUCULOSE KINASE FUCK
KeywordsTRANSFERASE / FUCOSE PROCESSING
Function / homology
Function and homology information


L-fuculokinase / L-fuculokinase activity / rhamnulokinase activity / rhamnose catabolic process
Similarity search - Function
Rhamnulokinase / : / 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 ...Rhamnulokinase / : / 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
Putative L-fuculose kinase fucK / Putative L-fuculose kinase fucK
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHiggins, M.A. / Suits, M.D.L. / Marsters, C. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus Pneumoniae.
Authors: Higgins, M.A. / Suits, M.D. / Marsters, C. / Boraston, A.B.
History
DepositionAug 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: L-FUCULOSE KINASE FUCK
B: L-FUCULOSE KINASE FUCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1963
Polymers107,1332
Non-polymers621
Water8,485471
1
A: L-FUCULOSE KINASE FUCK


Theoretical massNumber of molelcules
Total (without water)53,5671
Polymers53,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-FUCULOSE KINASE FUCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6292
Polymers53,5671
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.624, 60.624, 280.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein L-FUCULOSE KINASE FUCK / L-FUCULOSE KINASE


Mass: 53566.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97N88, UniProt: A0A0H2US93*PLUS, L-fuculokinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPOLYPEPTIDE A INCLUDES THE PRECEDING N-TERMINAL AFFINITY TAG. MET1 WAS NOT INCLUDED IN RECOMBINANT CONSTRUCT.

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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: 2.43 Å3/Da / Density % sol: 49.35 % / Description: NONE
Crystal growpH: 7.2
Details: SPFCSK AT A CONCENTRATION OF 24 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.2), 150 MM NACL, 1 MM MANGANESE CHLORIDE, AND 1 MM DTT WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION ...Details: SPFCSK AT A CONCENTRATION OF 24 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.2), 150 MM NACL, 1 MM MANGANESE CHLORIDE, AND 1 MM DTT WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION CONSISTING OF 4% (V PER V) ETHYLENE-GLYCOL, 100 MM 4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID (PH 7.5), AND 1.50 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2012 / Details: RH COATED
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.521
11K, H, -L20.479
ReflectionResolution: 2→37 Å / Num. obs: 67536 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CGK
Resolution: 2→36.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.988 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21597 3418 5.1 %RANDOM
Rwork0.16608 ---
obs0.16863 63900 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.896 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å20 Å20 Å2
2---3.71 Å20 Å2
3---7.43 Å2
Refinement stepCycle: LAST / Resolution: 2→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 4 471 7917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197633
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.96410340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91724.529340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.913151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1361538
X-RAY DIFFRACTIONr_chiral_restr0.1050.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.073.0593775
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0524.5794719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4813.3133858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 257 -
Rwork0.171 4725 -
obs--99.98 %

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