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- PDB-1rwa: Crystal structure of Arthrobacter aurescens chondroitin AC lyase -

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Basic information

Entry
Database: PDB / ID: 1rwa
TitleCrystal structure of Arthrobacter aurescens chondroitin AC lyase
Componentschondroitin AC lyase
KeywordsLYASE / chondroitinase / chondroitin lyase
Function / homology
Function and homology information


carbohydrate binding / lyase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / 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 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 ...Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / 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 / 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 / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chondroitinase (Chondroitin lyase)
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsLunin, V.V. / Li, Y. / Miyazono, H. / Kyogashima, M. / Bell, A.W. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism
Authors: Lunin, V.V. / Li, Y. / Linhardt, R.J. / Miyazono, H. / Kyogashima, M. / Kaneko, T. / Bell, A.W. / Cygler, M.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Feb 14, 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_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.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.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 AC lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8348
Polymers79,8641
Non-polymers9707
Water19,8711103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.356, 85.256, 82.162
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chondroitin AC lyase /


Mass: 79863.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrobacter aurescens (bacteria) / References: UniProt: P84141, chondroitin AC lyase
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1103 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293 K / pH: 6.4
Details: PEG 8000, ammonium acetate, glycerol, phosphate buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.005133, 1.009078, 0.997068
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0051331
21.0090781
30.9970681
ReflectionResolution: 1.3→50 Å / Num. obs: 183424 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rsym value: 0.067 / Net I/σ(I): 14.7
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.325 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→28.99 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.557 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1800 1 %RANDOM
Rwork0.134 ---
obs0.134 178604 100 %-
all-178604 --
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: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-0.07 Å2
2---0.95 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 27 1103 6730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215841
X-RAY DIFFRACTIONr_bond_other_d0.0010.025299
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.947949
X-RAY DIFFRACTIONr_angle_other_deg3.142312286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76223.333237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74315897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9571541
X-RAY DIFFRACTIONr_chiral_restr0.1830.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026609
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021205
X-RAY DIFFRACTIONr_nbd_refined0.2270.21182
X-RAY DIFFRACTIONr_nbd_other0.2930.25979
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.23044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2694
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3740.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8491.53739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47325979
X-RAY DIFFRACTIONr_scbond_it3.09132102
X-RAY DIFFRACTIONr_scangle_it4.0564.51970
X-RAY DIFFRACTIONr_rigid_bond_restr1.81825841
X-RAY DIFFRACTIONr_sphericity_free7.84921103
X-RAY DIFFRACTIONr_sphericity_bonded6.47425720
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 97
Rwork0.159 10795

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