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Basic information

Entry
Database: PDB / ID: 3krg
TitleStructural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase
ComponentsPectate lyase
KeywordsLYASE / Michaelis complex / hexasaccharide / pectate lyase / Calcium / Secreted
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsPickersgill, R.W. / To, T.T.
CitationJournal: Biochemistry / Year: 2010
Title: Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase
Authors: Seyedarabi, A. / To, T.T. / Ali, S. / Hussain, S. / Fries, M. / Madsen, R. / Clausen, M.H. / Teixteira, S. / Brocklehurst, K. / Pickersgill, R.W.
History
DepositionNov 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5264
Polymers43,3001
Non-polymers1,2263
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.626, 69.066, 59.656
Angle α, β, γ (deg.)90.00, 113.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pectate lyase / PL


Mass: 43300.059 Da / Num. of mol.: 1 / Mutation: D173A,N180A,K247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: pel / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39116, pectate lyase
#2: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 1074.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DGalpAa1-4DGalpAa1-4DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2112A-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, 50% PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→69.01 Å / Num. obs: 28827 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 8.608 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.067 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 18.3 / Num. unique all: 4138 / Rsym value: 0.067 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2O0V

2o0v


Resolution: 1.9→29.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.464 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1459 5.1 %RANDOM
Rwork0.132 ---
obs0.135 27344 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.69 Å2 / Biso mean: 8.969 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 80 723 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213213
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9484356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38325.068148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38415485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6671511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212463
X-RAY DIFFRACTIONr_mcbond_it0.7871.51968
X-RAY DIFFRACTIONr_mcangle_it1.44423156
X-RAY DIFFRACTIONr_scbond_it2.67631245
X-RAY DIFFRACTIONr_scangle_it3.6464.51200
LS refinement shellResolution: 0.129→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 107 -
Rwork0.13 2002 -
all-2109 -
obs-4138 95.86 %

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