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- PDB-1ofm: CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-... -

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Entry
Database: PDB / ID: 1ofm
TitleCRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE
ComponentsCHONDROITINASE B
KeywordsLYASE / ACTIVE SITE / BETA-ELIMINATION / CHONDROITIN 4-SULFATE
Function / homologyPectin lyase fold/virulence factor / Pectin lyase fold / PL-6 family / Chondroitinase B / chondroitin B lyase / chondroitin B lyase activity / Chondroitinase-B
Function and homology information
Specimen sourcePEDOBACTER HEPARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsMichel, G. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structure of Chondroitin B Lyase Complexed with Glycosaminoglycan Oligosaccharides Unravels a Calcium-Dependent Catalytic Machinery
Authors: Michel, G. / Pojasek, K. / Li, Y. / Sulea, T. / Linhardt, R. / Raman, R. / Prabhakar, V. / Sasisekharan, R. / Cygler, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 15, 2003 / Release: Apr 19, 2004
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 19, 2004Structure modelrepositoryInitial release
1.1Jan 23, 2013Structure modelAtomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
2.0Jun 14, 2017Structure modelAdvisory / Atomic model / Derived calculationsatom_site / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen_atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.type_symbol / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _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_sheet.id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHONDROITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88912
Polyers53,6891
Non-polymers2,20011
Water14,520806
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)50.537, 74.069, 58.989
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide CHONDROITINASE B


Mass: 53688.832 Da / Num. of mol.: 1
Details: HYDROXY-PROLINE AT N-TERMINUS GLYCOSYLATION AT SER234
Source: (gene. exp.) PEDOBACTER HEPARINUS (bacteria) / Production host: PEDOBACTER HEPARINUS (bacteria) / References: UniProt: Q46079, EC: 4.2.2.4

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Non-polymers , 11 types, 817 molecules

#2: Chemical ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#3: Chemical ChemComp-RAM / ALPHA-L-RHAMNOSE


Mass: 164.156 Da / Num. of mol.: 1 / Formula: C6H12O5 / Rhamnose
#4: Chemical ChemComp-GCU / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#5: Chemical ChemComp-XYP / BETA-D-XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 1 / Formula: C5H10O5
#6: Chemical ChemComp-MXZ / 6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE


Mass: 178.183 Da / Num. of mol.: 1 / Formula: C7H14O5
#7: Chemical ChemComp-GLA / ALPHA D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#8: Chemical ChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Glucose
#9: Chemical ChemComp-ASG / 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE


Mass: 301.271 Da / Num. of mol.: 2 / Formula: C8H15NO9S
#10: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#11: Chemical ChemComp-GCD / 4,5-DEHYDRO-D-GLUCURONIC ACID


Mass: 176.124 Da / Num. of mol.: 1 / Formula: C6H8O6
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Formula: H2O / Water

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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: 1.95 / Density percent sol: 34.9 %
Crystal growpH: 8.7
Details: PEG8000, 2-METHYL-2,4- PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.70

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Collection date: Nov 15, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 6.5 Å2 / D resolution high: 1.8 Å / D resolution low: 33.18 Å / Number obs: 40172 / Observed criterion sigma I: 0 / Rmerge I obs: 0.04 / NetI over sigmaI: 19.5 / Redundancy: 3.75 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.085 / Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 9.2 / Percent possible all: 1

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Processing

Software
NameVersionClassification
CNS1.0refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DBG
R Free selection details: RANDOM / Data cutoff high absF: 1399907.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 41.4551 / Solvent model param ksol: 0.309859
Displacement parametersB iso mean: 12.8 Å2 / Aniso B11: -0.68 Å2 / Aniso B12: 0 Å2 / Aniso B13: -1.01 Å2 / Aniso B22: 0.21 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.47 Å2
Least-squares processR factor R free: 0.183 / R factor R free error: 0.004 / R factor R work: 0.142 / R factor obs: 0.142 / Highest resolution: 1.8 Å / Lowest resolution: 33.18 Å / Number reflection R free: 2010 / Number reflection obs: 40151 / Percent reflection R free: 5 / Percent reflection obs: 99.6
Refine analyzeLuzzati coordinate error free: 0.18 Å / Luzzati coordinate error obs: 0.14 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.04 Å
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 33.18 Å
Number of atoms included #LASTProtein: 3784 / Nucleic acid: 0 / Ligand: 135 / Solvent: 806 / Total: 4725
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
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
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.18 / R factor R free error: 0.01 / R factor R work: 0.138 / Lowest resolution: 1.91 Å / Number reflection R free: 302 / Number reflection R work: 6279 / Total number of bins used: 6 / Percent reflection R free: 4.6 / Percent reflection obs: 98.6
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.PARAM

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