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- PDB-2c4s: CALCIUM CHONDROITIN 4-SULFATE. MOLECULAR CONFORMATION AND ORGANIZ... -

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Entry
Database: PDB / ID: 2c4s
TitleCALCIUM CHONDROITIN 4-SULFATE. MOLECULAR CONFORMATION AND ORGANIZATION OF POLYSACCHARIDE CHAINS IN A PROTEOGLYCAN
Components
  • (0) x 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranuronic acid
  • (1) x CALCIUM ION
  • (2) x water
KeywordsTEXTURE OF CONNECTIVE TISSUE
MethodFIBER DIFFRACTION / Resolution: 3 Å
AuthorsArnott, S.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: Calcium chondroitin 4-sulfate: molecular conformation and organization of polysaccharide chains in a proteoglycan.
Authors: Cael, J.J. / Winter, W.T. / Arnott, S.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1978
Title: Lals, a Linked-Atom Least-Squares Reciprocal-Space Refinement System Incorporating Stereochemical Restraints to Supplement Sparse Diffraction Data
Authors: Smith, P.J.C. / Arnott, S.
History
DepositionMay 23, 1978Processing site: BNL
Revision 1.0Mar 28, 1980Provider: repository / Type: Initial release
Revision 1.1Mar 21, 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 / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0173
Polymers00
Non-polymers1,0173
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)7.450, 17.810, 19.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
DetailsTHE FOUR-RESIDUE CHAIN SEGMENT GIVEN HERE WAS OBTAINED FROM THE PUBLISHED COORDINATES FOR A TWO-RESIDUE FRAGMENT BY THE ACTION OF A 21 SCREW AXIS AS DEFINED IN THE PAPER CITED IN THE JRNL RECORDS ABOVE.

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Components

#1: Polysaccharide 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2- ...2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 936.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAc[4S]b1-4DGlcpAa1-3DGalpNAc[4S]b1-4DGlcpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122A-1a_1-5][a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O]/1-2-1-2/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-3-deoxy-GalpNAc4SO3]{}}}}LINUCSPDB-CARE
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Data collection

Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
LINKED-ATOMLEAST-SQUARES MODEL-BUILDING PROCEDURErefinement
LALSrefinement
RefinementHighest resolution: 3 Å
Details: THE SPACE GROUP CHOSEN FOR THIS STUDY WAS P 2 21 21 WHICH IS A NON-STANDARD REPRESENTATION OF P 21 21 2. IN THIS FORMER GROUP THE EQUIPOINTS ARE X,Y,Z X,-Y,-Z -X,1/2-Y, 1/2+Z AND -X,1/2+Y,1/2-Z.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 62 14 76

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