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- PDB-2x03: The X-ray structure of the Streptomyces coelicolor A3 Chondroitin... -

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Basic information

Entry
Database: PDB / ID: 2x03
TitleThe X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase Y253A mutant
ComponentsPUTATIVE SECRETED LYASE
KeywordsLYASE / HYALURONATE LYASE / CHONDROITIN LYASE / FAMILY 8
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
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 / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal ...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 / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsElmabrouk, Z.H. / Taylor, E.J. / Vincent, F. / Smith, N.L. / Turkenburg, J.P. / Davies, G.J. / Black, G.W.
CitationJournal: Proteins / Year: 2011
Title: Crystal Structures of a Family 8 Polysaccharide Lyase Reveal Open and Highly Occluded Substrate-Binding Cleft Conformations.
Authors: Elmabrouk, Z.H. / Vincent, F. / Zhang, M. / Smith, N.L. / Turkenburg, J.P. / Charnock, S.J. / Black, G.W. / Taylor, E.J.
History
DepositionDec 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE SECRETED LYASE
B: PUTATIVE SECRETED LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8853
Polymers165,8602
Non-polymers241
Water15,151841
1
A: PUTATIVE SECRETED LYASE


Theoretical massNumber of molelcules
Total (without water)82,9301
Polymers82,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE SECRETED LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9542
Polymers82,9301
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)317.095, 317.095, 82.976
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PUTATIVE SECRETED LYASE / PL8


Mass: 82930.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-776 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A3(2)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM NO. 40783
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O86516, hyaluronate lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 264 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 264 TO ALA
Sequence detailsTHE CLONED SEQUENCE CONTAINS AN N-TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IS NOT ...THE CLONED SEQUENCE CONTAINS AN N-TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IS NOT ORDERED IN THE STRUCTURE. THERE IS ALSO A SINGLE RESIDUE MUTATION Y253A.

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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: 4.8 Å3/Da / Density % sol: 74.6 % / Description: NONE
Crystal growDetails: 4.0M NA FORMATE WITH 20% GLYCEROL AS A CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→59.8 Å / Num. obs: 138108 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 13.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDA

2wda


Resolution: 2.3→158.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.16 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22757 6933 5 %RANDOM
Rwork0.19447 ---
obs0.19612 131167 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→158.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11349 0 1 841 12191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02111743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.92916062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68251497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08721.562525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.227151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.47215132
X-RAY DIFFRACTIONr_chiral_restr0.1650.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219222
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1111.57387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.943211794
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.28734356
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0434.54268
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 516 -
Rwork0.236 9681 -
obs--99.97 %

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