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- PDB-1dyp: 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: 1dyp
Title1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE
ComponentsKAPPA-CARRAGEENASE
KeywordsHYDROLASE / KAPPA-CARRAGEENAN DOUBLE HELIX DEGRADATION
Function / homology
Function and homology information


kappa-carrageenase / kappa-carrageenase activity / carbohydrate metabolic process / periplasmic space
Similarity search - Function
Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 ...Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Kappa-carrageenase
Similarity search - Component
Biological speciesPSEUDOALTEROMONAS CARRAGEENOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å
AuthorsMichel, G. / Chantalat, L. / Dideberg, O.
Citation
Journal: Structure / Year: 2001
Title: The Kappa-Carrageenase of P. Carrageenovora Features a Tunnel-Shaped Active Site: A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases
Authors: Michel, G. / Chantalat, L. / Duee, E. / Barbeyron, T. / Henrissat, B. / Kloareg, B. / Dideberg, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Kappa-Carrageenase from Pseudoalteromonas Carrageenovora.
Authors: Michel, G. / Barbeyron, T. / Flament, D. / Vernet, T. / Kloareg, B. / Dideberg, O.
History
DepositionFeb 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...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 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KAPPA-CARRAGEENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,59415
Polymers31,5591
Non-polymers1,03514
Water7,296405
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.408, 61.120, 75.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KAPPA-CARRAGEENASE


Mass: 31559.338 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CADMIUM CHLORIDE
Source: (gene. exp.) PSEUDOALTEROMONAS CARRAGEENOVORA (bacteria)
Description: PROCESSED PROTEIN, HIS-TAG, SELEMETHIONYL PROTEIN
Gene: CGKA / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P43478, kappa-carrageenase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
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: 2.019 Å3/Da / Density % sol: 40.38 %
Crystal growpH: 4.5 / Details: pH 4.50
Crystal grow
*PLUS
Temperature: 285 K / pH: 7.2 / Method: vapor diffusion, hanging drop
Details: Michel, G., (1999) Acta Crystallogr.,Sect.D, D55, 918.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
210 mMTris-HCl1drop
3200 mM1dropNaCl
40.1 Msodium acetate1reservoir
530 %PEG40001reservoir
650 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8860, 0.9755, 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8861
20.97551
30.97871
ReflectionResolution: 1.54→24.25 Å / Num. obs: 38205 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.1
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.116 / % possible all: 81.3
Reflection
*PLUS
Redundancy: 3.15 % / Num. measured all: 120447 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 1.54→24.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1371908.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING RESIDUES HAVE TWO CONFORMATIONS, MET 28, SER 199, LYS 277, SER 285, GLU 287.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1919 5 %RANDOM
Rwork0.178 ---
obs0.178 38205 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.427 Å2 / ksol: 0.33629 e/Å3
Displacement parametersBiso mean: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2--1.85 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.54→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 14 405 2625
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.31.5
X-RAY DIFFRACTIONc_mcangle_it0.532
X-RAY DIFFRACTIONc_scbond_it0.452
X-RAY DIFFRACTIONc_scangle_it0.682.5
LS refinement shellResolution: 1.54→1.64 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 265 4.8 %
Rwork0.206 5240 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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