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- PDB-4c24: L-fuculose 1-phosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 4c24
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
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: 1.5 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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.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)24,6057
Polymers24,1351
Non-polymers4706
Water1,838102
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)98,42028
Polymers96,5384
Non-polymers1,88224
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 area11990 Å2
ΔGint-386.2 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.970, 112.970, 40.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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: 24134.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q04I08, UniProt: A0A0H2US48*PLUS, L-fuculose-phosphate aldolase

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Non-polymers , 6 types, 108 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-SO4 / SULFATE ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 102 / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.755
11K, H, -L20.245
ReflectionResolution: 1.5→36 Å / Num. obs: 41479 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 9.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUA

2fua


Resolution: 1.5→35.72 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.537 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.011 / 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
Rfree0.16066 2157 5.2 %RANDOM
Rwork0.13952 ---
obs0.14062 39302 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.271 Å2
Baniso -1Baniso -2Baniso -3
1--9.65 Å20 Å20 Å2
2---9.65 Å20 Å2
3---19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 22 102 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9742346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1765232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6932572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83315299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.61157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211279
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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_restr3.38331720
X-RAY DIFFRACTIONr_sphericity_free25.296529
X-RAY DIFFRACTIONr_sphericity_bonded11.56451760
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 155 -
Rwork0.163 2831 -
obs--99.17 %

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