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- PDB-1h80: 1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE- 3,6-ANHYDRO-D-GALACTOSE... -

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Basic information

Entry
Database: PDB / ID: 1h80
Title1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE- 3,6-ANHYDRO-D-GALACTOSE-2-SULFATE 4 GALACTOHYDROLASE
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
Biological speciesALTEROMONAS SP. ATCC43554 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMichel, G. / Chantalat, L. / Dideberg, O.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Expression, Purification, Cristallization and Preliminary X-Ray Analysis of the Iota-Carrageenase from Alteromonas Fortis
Authors: Michel, G. / Flament, D. / Barbeyron, T. / Vernet, T. / Kloareg, B. / Dideberg, O.
History
DepositionJan 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_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_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_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.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

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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)104,87422
Polymers103,8722
Non-polymers1,00220
Water19,9971110
1
A: IOTA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,43711
Polymers51,9361
Non-polymers50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IOTA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,43711
Polymers51,9361
Non-polymers50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.870, 90.070, 124.120
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9928, 0.08692, 0.08239), (0.08627, -0.99621, 0.01139), (0.08307, -0.0042, -0.99653)
Vector: -6.86677, -14.89559, 181.71701)

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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
Details: COMPLEXED WITH CALCIUM, SODIUM AND CHLORIDE / Source: (gene. exp.) ALTEROMONAS SP. ATCC43554 (bacteria) / Description: HIS-TAG, SELEMETHIONYL PROTEIN. / Gene: CGIA / Plasmid: PET20B / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): B834(DE3) / References: UniProt: Q9F5I8, iota-carrageenase

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Non-polymers , 5 types, 1130 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1110 / 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 % / Description: MAD DATA COLLECTION ON BM30
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE PH 6.5, 10% GLYCEROL, 15-17% PEG6000, 200MM CALCIUM ACETATE
Crystal grow
*PLUS
Temperature: 288 K / Method: vapor diffusion, hanging drop
Details: Michel, G., (2000) Acta Crystallogr.,Sect.D, 56, 766.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
210 mMTris-HCl1droppH7.2
3200 mM1dropNaCl
41 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 762046 / % possible obs: 97.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.123
Reflection shellResolution: 1.6→1.66 Å / Rsym value: 0.203 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 1.6 Å / Redundancy: 4.8 % / Num. measured all: 157467 / Rmerge(I) obs: 0.123
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.203

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1960016.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DOMAIN A HAS A HIGHER B FACTOR, REGIONS 314 - 334 AND 341 - 350 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.223 7885 5 %RANDOM
Rwork0.207 ---
obs0.207 156297 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2073 Å2 / ksol: 0.415064 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å2-0.35 Å2
2---2.34 Å20 Å2
3---0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 50 1110 7942
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.811.5
X-RAY DIFFRACTIONc_mcangle_it1.282
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 1300 5.1 %
Rwork0.215 24418 -
obs--96 %
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 DIFFRACTION4GLYCEROLGLYCEROL
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Lowest resolution: 1.66 Å

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