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- PDB-1ktw: IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS -

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Basic information

Entry
Database: PDB / ID: 1ktw
TitleIOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS
ComponentsIOTA-CARRAGEENASE
KeywordsHYDROLASE / IOTA-CARRAGEENAN DOUBLE HELIX DEGRADATION
Function / homology
Function and homology information


iota-carrageenase / iota-carrageenase activity / polysaccharide catabolic process / cell wall organization / extracellular region
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
: / Iota-carrageenase
Similarity search - Component
Biological speciesAlteromonas sp. ATCC 43554 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMichel, G. / Kahn, R. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Structural Bases of the Processive Degradation of iota-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae.
Authors: Michel, G. / Helbert, W. / Kahn, R. / Dideberg, O. / Kloareg, B.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: The Iota-Carrageenase of Alteromonas Fortis. A Beta-Helix Fold-Containing Enzyme for the Degradation of a Highly Polyanionic Polysaccharide
Authors: Michel, G. / Chantalat, L. / Fanchon, E. / Henrissat, B. / Kloareg, B. / Dideberg, O.
History
DepositionJan 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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_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_leaving_atom_flag / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IOTA-CARRAGEENASE
B: IOTA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,87120
Polymers103,8722
Non-polymers1,99918
Water9,404522
1
A: IOTA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65311
Polymers51,9361
Non-polymers1,71710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IOTA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2189
Polymers51,9361
Non-polymers2828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.730, 122.310, 91.941
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IOTA-CARRAGEENASE


Mass: 51936.082 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 28-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas sp. ATCC 43554 (bacteria) / Plasmid: PET20B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 10039456, UniProt: Q9F5I8*PLUS, iota-carrageenase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 484.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6_2*OSO/3=O/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp4SO3]{[(3+1)]{}}LINUCSPDB-CARE
#3: Polysaccharide 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6- ...3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 950.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6_2*OSO/3=O/3=O]/1-2-1-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][<C12O15S2>]{[(1+1)][b-D-Galp4SO3]{[(3+1)]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 538 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, 200mM calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoirpH6.5
315-17 %(w/v)PEG60001reservoir
4200 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 / Wavelength: 0.9 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2000 / Details: MIRRORS
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.91
ReflectionResolution: 2→20 Å / Num. obs: 79185 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 9.2 Å2 / Rsym value: 0.036
Reflection shellResolution: 2→2.05 Å / Rsym value: 0.079 / % possible all: 88.4
Reflection
*PLUS
Redundancy: 1.93 % / Num. measured all: 153545 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H80

1h80


Resolution: 2→23.17 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1943861.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3986 5 %RANDOM
Rwork0.203 ---
all-79185 --
obs-79185 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.8607 Å2 / ksol: 0.43487 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å21.71 Å2
2---1.93 Å20 Å2
3---0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 0 105 522 7837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 645 5.4 %
Rwork0.206 11306 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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