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- PDB-1gxm: Family 10 polysaccharide lyase from Cellvibrio cellulosa -

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Basic information

Entry
Database: PDB / ID: 1gxm
TitleFamily 10 polysaccharide lyase from Cellvibrio cellulosa
ComponentsPECTATE LYASE
KeywordsLYASE / PECTATE / ELIMINATION
Function / homology
Function and homology information


polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / lyase activity
Similarity search - Function
Pectic acid lyase / Pectic acid lyase / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate binding module (family 6) / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily ...Pectic acid lyase / Pectic acid lyase / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate binding module (family 6) / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCELLVIBRIO CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.32 Å
AuthorsCharnock, S.J. / Brown, I.E. / Turkenburg, J.P. / Black, G.W. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Convergent Evolution Sheds Light on the Anti-Beta-Elimination Mechanism Common to Family 1 and 10 Polysaccharide Lyases
Authors: Charnock, S.J. / Brown, I.E. / Turkenburg, J.P. / Black, G.W. / Davies, G.J.
History
DepositionApr 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: PECTATE LYASE
B: PECTATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7926
Polymers73,4232
Non-polymers3684
Water15,043835
1
A: PECTATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9884
Polymers36,7121
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PECTATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8042
Polymers36,7121
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 106.113, 55.365
Angle α, β, γ (deg.)90.00, 91.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99956, 0.02751, 0.01066), (0.02785, -0.99907, -0.03289), (0.00974, 0.03317, -0.9994)
Vector: -2.46408, 142.66696, 80.98895)

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Components

#1: Protein PECTATE LYASE / POLYGALACTURONIC ACID LYASE


Mass: 36711.668 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 327-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: Q9F7L3, pectate lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 835 / 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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASE DIFFUSION USING THE HANGING-DROP METHOD WITH SCREENING AS DESCRIBED BY BRZOZOWSKI & WALTON (2001 [[BRZOZOWSKI, A.M. & WALTON, J. (2001). J. ...Details: CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASE DIFFUSION USING THE HANGING-DROP METHOD WITH SCREENING AS DESCRIBED BY BRZOZOWSKI & WALTON (2001 [[BRZOZOWSKI, A.M. & WALTON, J. (2001). J. APPL. CRYST. 34, 97-101.]] ). THE PROTEIN CONCENTRATION WAS 30 MG ML-1 IN NA MES BUFFER PH 5.2 CONTAINING KSCN AT A CONCENTRATION OF 200 MM. THE PRECIPITANT WAS 20%(W/V) MONOMETHYL POLYETHYLENEGLYCOL 2000 AND CRYSTALS APPEARED AFTER 2 D AT 291 K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: Charnock, S.J., (2001) Acta Crystallogr., D57, 1141.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
3200 mM1dropKSCN
420 %(w/v)PEG2000 MME1reservoir
2sodium MES1droppH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9366
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9366 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 112216 / % possible obs: 86.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.4 / % possible all: 35.4
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.32→15.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.772 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 5557 5 %RANDOM
Rwork0.13 ---
obs0.132 106610 86.5 %-
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: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.48 Å2
2---0.34 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.32→15.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 24 835 5986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215334
X-RAY DIFFRACTIONr_bond_other_d0.0030.024555
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9247219
X-RAY DIFFRACTIONr_angle_other_deg1.916310614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40423.86272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75315842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined0.2310.21272
X-RAY DIFFRACTIONr_nbd_other0.2750.25606
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.23013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.278
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.53235
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59925169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12632099
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1684.52050
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: 1.32→1.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 152
Rwork0.183 3216
Refinement
*PLUS
Rfactor Rfree: 0.162 / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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