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- PDB-4ew9: The liganded structure of C. bescii family 3 pectate lyase -

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Basic information

Entry
Database: PDB / ID: 4ew9
TitleThe liganded structure of C. bescii family 3 pectate lyase
ComponentsPectate lyase
KeywordsLYASE / PL3 / PARALLEL BETA-HELIX
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / hydrolase activity / extracellular region / membrane / metal ion binding
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / 3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / alpha-D-galactopyranuronic acid / D-galacturonic acid / pectate lyase
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction.
Authors: Alahuhta, M. / Brunecky, R. / Chandrayan, P. / Kataeva, I. / Adams, M.W. / Himmel, M.E. / Lunin, V.V.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 1, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,30622
Polymers42,0672
Non-polymers2,23820
Water6,738374
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,38813
Polymers21,0341
Non-polymers1,35412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9189
Polymers21,0341
Non-polymers8848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Pectate lyase
hetero molecules

B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,30622
Polymers42,0672
Non-polymers2,23820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454x-1/2,y+1/2,z-11
Buried area4130 Å2
ΔGint-144 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.946, 35.898, 98.687
Angle α, β, γ (deg.)90.00, 132.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pectate lyase


Mass: 21033.727 Da / Num. of mol.: 2 / Fragment: UNP residues 268-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (bacteria) / Strain: DSM 6725 / Z-1320 / Gene: Athe_1854 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKT4, pectate lyase

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Sugars , 3 types, 5 molecules

#2: Polysaccharide 4-deoxy-beta-L-threo-hex-4-enopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 352.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112A-1a_1-5][a21eEA-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-DGU / D-galacturonic acid / D-Galacturonate


Type: D-saccharide / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
#6: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 389 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 70% v/v (+/-)-2-Methyl 2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 11, 2011 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 47595 / Num. obs: 47595 / % possible obs: 99.9 % / Redundancy: 4.83 % / Rsym value: 0.0584 / Net I/σ(I): 13.62
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.01 % / Mean I/σ(I) obs: 2.74 / Num. unique all: 7847 / Rsym value: 0.3498 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.6.0117refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3T9G

3t9g


Resolution: 1.6→33.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.858 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20374 2368 5.1 %RANDOM
Rwork0.16378 ---
obs0.16584 44501 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.436 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-1.51 Å2
2--1.3 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 136 374 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193329
X-RAY DIFFRACTIONr_bond_other_d0.0030.022112
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.9634564
X-RAY DIFFRACTIONr_angle_other_deg1.10435280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37527.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5215561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.323152
X-RAY DIFFRACTIONr_chiral_restr0.1340.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02582
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 167 -
Rwork0.257 3026 -
obs--94.36 %

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