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- PDB-4c25: L-fuculose 1-phosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 4c25
TitleL-fuculose 1-phosphate aldolase
ComponentsL-FUCULOSE PHOSPHATE ALDOLASE
KeywordsLYASE / FUCOSE PROCESSING
Function / homology
Function and homology information


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / pentose catabolic process / metal ion binding / cytosol
Similarity search - Function
: / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / NICKEL (II) ION / L-fuculose phosphate aldolase / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 18, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _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: L-FUCULOSE PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2149
Polymers23,5461
Non-polymers6698
Water1,820101
1
A: L-FUCULOSE PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,85836
Polymers94,1844
Non-polymers2,67432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13730 Å2
ΔGint-341.8 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.490, 113.490, 41.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2089-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-FUCULOSE PHOSPHATE ALDOLASE / L-FUCULOSE 1-PHOSPHATE ALDOLASE


Mass: 23545.959 Da / Num. of mol.: 1
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: Q97N89, UniProt: A0A0H2US48*PLUS, L-fuculose-phosphate aldolase

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Non-polymers , 7 types, 109 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPOLYPEPTIDE INCLUDES A PORTION OF THE PRECEDING N-TERMINAL AFFINITY TAG

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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: 2.77 Å3/Da / Density % sol: 55.7 % / Description: NONE
Crystal growpH: 8
Details: SPFCSA AT A CONCENTRATION OF 14 MG PER ML, BUFFERED IN 20 MM TRIS-HCL (PH 8.0) AND 5 MM DITHIOTHREITOL (DTT) WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION OF 4% (V PER V) ...Details: SPFCSA AT A CONCENTRATION OF 14 MG PER ML, BUFFERED IN 20 MM TRIS-HCL (PH 8.0) AND 5 MM DITHIOTHREITOL (DTT) WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION OF 4% (V PER V) GLYCEROL, 1.50 M AMMONIUM SULPHATE, 100 MM TRIS-HCL (PH 8.5) AND 8 MM ZINC CHLORIDE.

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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
ReflectionResolution: 2.03→40 Å / Num. obs: 15800 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUA

2fua


Resolution: 2.03→80.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.778 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27799 924 5.4 %RANDOM
Rwork0.22312 ---
obs0.22617 16234 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.03→80.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 35 101 1771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9782338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29725.26376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18215297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.007157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211287
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_it2.5343.706870
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7175.551089
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3523.945859
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.19131.3692796
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: 2.031→2.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 74 -
Rwork0.488 1183 -
obs--99.76 %

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