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- PDB-4a34: Crystal structure of the fucose mutarotase in complex with L-fuco... -

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Basic information

Entry
Database: PDB / ID: 4a34
TitleCrystal structure of the fucose mutarotase in complex with L-fucose from Streptococcus pneumoniae
ComponentsRBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
KeywordsISOMERASE
Function / homology
Function and homology information


D-ribose pyranase / D-ribose pyranase activity / fucosylation / monosaccharide metabolic process / racemase and epimerase activity, acting on carbohydrates and derivatives / fucose binding / fucose metabolic process / monosaccharide binding
Similarity search - Function
: / RbsD-like fold / RbsD-like domain / D-ribose pyranase RbsD/L-fucose mutarotase FucU / RbsD-like superfamily / RbsD / FucU transport protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-L-fucopyranose / : / RbsD/FucU transport protein family protein / D-ribose pyranase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsHiggins, M.A. / Boraston, A.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the Fucose Mutarotase from Streptococcus Pneumoniae in Complex with L-Fucose
Authors: Higgins, M.A. / Boraston, A.B.
History
DepositionSep 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Sep 4, 2013Group: Atomic model / Derived calculations
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_auth_seq_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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
B: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
C: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
D: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
E: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
F: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
G: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
H: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
I: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
J: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
K: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
L: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
M: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
N: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
O: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
P: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
Q: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
R: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
S: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
T: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,15650
Polymers331,48220
Non-polymers3,67430
Water15,313850
1
A: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
B: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
C: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
D: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
E: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
F: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
G: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
H: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
I: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
J: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,57825
Polymers165,74110
Non-polymers1,83715
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26720 Å2
ΔGint-106.2 kcal/mol
Surface area51480 Å2
MethodPISA
2
K: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
L: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
M: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
N: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
O: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
P: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
Q: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
R: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
S: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
T: RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,57825
Polymers165,74110
Non-polymers1,83715
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25180 Å2
ΔGint-102.9 kcal/mol
Surface area52330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.319, 144.158, 165.460
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RBSD/FUCU TRANSPORT PROTEIN FAMILY PROTEIN / FUCOSE MUTAROTASE


Mass: 16574.094 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04I09, UniProt: A0A0H2ZNZ5*PLUS
#2: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.39 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU AREA DETECTOR / Details: OSMIC 'BLUE'
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 97486 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→19.97 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.176 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.081 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29174 5139 5 %RANDOM
Rwork0.22482 ---
obs0.22822 97486 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.226 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21686 0 230 850 22766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02222316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.99530308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91352783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6224.597881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68153880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4511598
X-RAY DIFFRACTIONr_chiral_restr0.0830.23611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116218
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_it0.4121.513927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.779222522
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.04738389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7314.57786
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 373 -
Rwork0.346 7007 -
obs--98.74 %

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