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- PDB-1hn0: CRYSTAL STRUCTURE OF CHONDROITIN ABC LYASE I FROM PROTEUS VULGARI... -

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Basic information

Entry
Database: PDB / ID: 1hn0
TitleCRYSTAL STRUCTURE OF CHONDROITIN ABC LYASE I FROM PROTEUS VULGARIS AT 1.9 ANGSTROMS RESOLUTION
ComponentsCHONDROITIN ABC LYASE I
KeywordsLYASE / chondroitinase ABC I / chonroitin digestion
Function / homology
Function and homology information


chondroitin-sulfate-ABC endolyase / chondroitin-sulfate-ABC endolyase activity / glycosaminoglycan catabolic process / carbohydrate binding / carbohydrate metabolic process / periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Lyase, N-terminal / Lyase, catalytic / Chondroitin sulfate ABC endolyase / Chondroitin sulfate ABC lyase / Lyase, N terminal / Lyase, catalytic / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain ...Lyase, N-terminal / Lyase, catalytic / Chondroitin sulfate ABC endolyase / Chondroitin sulfate ABC lyase / Lyase, N terminal / Lyase, catalytic / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Galactose-binding lectin / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Distorted Sandwich / Jelly Rolls / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chondroitin sulfate ABC endolyase
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 1.9 Å
AuthorsHuang, W. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Proteus vulgaris Chondroitin Sulfate ABC Lyase I at 1.9 Angstroms Resolution
Authors: Huang, W. / Lunin, V.V. / Li, Y. / Suzuki, S. / Sugiura, N. / Miyazono, H. / Cygler, M.
History
DepositionDec 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHONDROITIN ABC LYASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2392
Polymers115,2161
Non-polymers231
Water30,0131666
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.280, 95.140, 229.950
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 CHONDROITIN ABC LYASE I


Mass: 115216.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Proteus vulgaris (bacteria) / Strain: NCTC 4636 / References: UniProt: P59807, EC: 4.2.2.4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1666 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, amonium acetate, magnesium acetate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG33501reservoir
20.2 Mammonium acetate1reservoir
30.2 Mmagnesium acetate1reservoir
40.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.006 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 1999 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 77350 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5
Reflection shellHighest resolution: 1.9 Å / Rmerge(I) obs: 0.248 / % possible all: 82.4
Reflection
*PLUS
Num. obs: 78220 / % possible obs: 91.3 % / Num. measured all: 805344
Reflection shell
*PLUS
% possible obs: 82.4 %

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
SCALEPACKdata scaling
CNSrefinement
CNSphasing
DENZOdata reduction
RefinementMethod to determine structure: MAD, MIR / Resolution: 1.9→19.88 Å / SU B: 3.024 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21224 1548 2 %RANDOM
Rwork0.15642 ---
obs0.15753 75799 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 1 1666 9426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.93410789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.891151356
X-RAY DIFFRACTIONr_chiral_restr0.1070.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026082
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.24007
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.21360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.2113
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.54841
X-RAY DIFFRACTIONr_mcangle_it1.50727821
X-RAY DIFFRACTIONr_scbond_it2.40333112
X-RAY DIFFRACTIONr_scangle_it3.7284.52968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.905→1.954 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 98
Rwork0.161 4873
Software
*PLUS
Name: REFMAC / Version: 5.1.08 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. reflection obs: 75800 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.44
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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