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- PDB-4c21: L-Fucose Isomerase In Complex With Fucitol -

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Basic information

Entry
Database: PDB / ID: 4c21
TitleL-Fucose Isomerase In Complex With Fucitol
ComponentsL-FUCOSE ISOMERASE
KeywordsISOMERASE / FUCOSE PROCESSING
Function / homology
Function and homology information


L-fucose isomerase / L-fucose isomerase activity / arabinose isomerase activity / D-arabinose catabolic process / L-fucose catabolic process / manganese ion binding / cytoplasm
Similarity search - Function
L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily ...L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily / L-fucose isomerase, domain 2 superfamily / L-fucose isomerase, domain 3 superfamily / L-fucose isomerase, C-terminal domain / L-fucose isomerase, first N-terminal domain / L-fucose isomerase, second N-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FUCITOL / : / L-fucose isomerase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / software / struct_conn / struct_sheet / 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_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_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 / _software.name / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,08622
Polymers135,6512
Non-polymers1,43520
Water12,250680
1
A: L-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
hetero molecules

A: L-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
hetero molecules

A: L-FUCOSE ISOMERASE
B: L-FUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,25966
Polymers406,9536
Non-polymers4,30660
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area47520 Å2
ΔGint-209.5 kcal/mol
Surface area121280 Å2
MethodPQS
Unit cell
Length a, b, c (Å)152.850, 152.850, 408.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2330-

HOH

21B-2280-

HOH

31B-2337-

HOH

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Components

#1: Protein L-FUCOSE ISOMERASE / 6-DEOXY-L-GALACTOSE ISOMERASE / FUCIASE


Mass: 67825.578 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: Q97N97, L-fucose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FOC / FUCITOL


Mass: 166.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMOLECULE B INCLUDES THE N-TERMINAL 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: 3.44 Å3/Da / Density % sol: 64.27 % / Description: NONE
Crystal growpH: 8
Details: SPFCSI AT A CONCENTRATION OF 12 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.0), 150 MM NACL, AND 2 MM DTT WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUMES OF 100 MM TRIS-HCL (PH 8.0), 27% (W PER ...Details: SPFCSI AT A CONCENTRATION OF 12 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.0), 150 MM NACL, AND 2 MM DTT WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUMES OF 100 MM TRIS-HCL (PH 8.0), 27% (W PER V) POLYETHYLENE GLYCOL 4,000, 50 MM NACL, AND 200 MM MAGNESIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03318
DetectorType: MARRESEARCH MX-300HE / Detector: CCD / Date: Mar 27, 2012
Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT)
RadiationMonochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 59825 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.3 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUI

1fui


Resolution: 2.55→49.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.172 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.206 / 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
Rfree0.1875 3022 5.1 %RANDOM
Rwork0.13518 ---
obs0.13785 56803 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.132 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.79 Å20 Å2
2--0.79 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9364 0 88 680 10132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.94913092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40851190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52123.607463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0711572
X-RAY DIFFRACTIONr_chiral_restr0.1070.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217472
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_it2.6533.1844766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.834.7635954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9953.3924905
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: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 198 -
Rwork0.22 4038 -
obs--96.1 %

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