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- PDB-5ocq: Crystal structure of the complex of the kappa-carrageenase from P... -

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Basic information

Entry
Database: PDB / ID: 5ocq
TitleCrystal structure of the complex of the kappa-carrageenase from Pseudoalteromonas carrageenovora with an oligotetrasaccharide of kappa-carrageenan
ComponentsKappa-carrageenase
KeywordsHYDROLASE / Glycoside hydrolase / kappa-carrageenase / beta jellyroll / marine carbohydrase
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
CITRIC ACID / Kappa-carrageenase
Similarity search - Component
Biological speciesPseudoalteromonas carrageenovora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCzjzek, M. / Leroux, C. / Bernard, T. / Matard-Mann, M. / Jeudy, A. / Michel, G.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights into marine carbohydrate degradation by family GH16 kappa-carrageenases.
Authors: Matard-Mann, M. / Bernard, T. / Leroux, C. / Barbeyron, T. / Larocque, R. / Prechoux, A. / Jeudy, A. / Jam, M. / Nyvall Collen, P. / Michel, G. / Czjzek, M.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
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.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _pdbx_struct_assembly_gen.asym_id_list / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kappa-carrageenase
B: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9036
Polymers65,9372
Non-polymers1,9664
Water10,539585
1
A: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9513
Polymers32,9691
Non-polymers9832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9513
Polymers32,9691
Non-polymers9832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.608, 67.364, 158.399
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: 32968.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas carrageenovora (bacteria)
Gene: cgkA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P43478, kappa-carrageenase
#2: Polysaccharide 3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha- ...3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 790.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][<C12O12S1>]{[(1+1)][b-D-Galp4SO3]{[(3+1)]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.0 M sodium citrate, 100 mM cacodylate pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→79 Å / Num. obs: 74710 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.966 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.071 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 25328 / Rsym value: 0.155 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYP

1dyp


Resolution: 1.7→34.65 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.424 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16575 3733 5 %RANDOM
Rwork0.13572 ---
obs0.13727 70361 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 128 585 5206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194842
X-RAY DIFFRACTIONr_bond_other_d0.0020.024352
X-RAY DIFFRACTIONr_angle_refined_deg2.3781.9366585
X-RAY DIFFRACTIONr_angle_other_deg2.537310058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64824.204245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0191525
X-RAY DIFFRACTIONr_chiral_restr0.2430.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021194
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_it1.4361.0482202
X-RAY DIFFRACTIONr_mcbond_other1.4311.0472201
X-RAY DIFFRACTIONr_mcangle_it2.1321.5642750
X-RAY DIFFRACTIONr_mcangle_other2.1351.5652751
X-RAY DIFFRACTIONr_scbond_it2.6031.3042640
X-RAY DIFFRACTIONr_scbond_other2.5971.3022638
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8211.8573830
X-RAY DIFFRACTIONr_long_range_B_refined5.7639.8145574
X-RAY DIFFRACTIONr_long_range_B_other5.3249.1185310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 293 -
Rwork0.148 5101 -
obs--99.61 %

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