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- PDB-2v8k: Structure of a Family 2 Pectate Lyase in Complex with Trigalactur... -

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Basic information

Entry
Database: PDB / ID: 2v8k
TitleStructure of a Family 2 Pectate Lyase in Complex with Trigalacturonic Acid
ComponentsPECTATE LYASE
KeywordsLYASE / PECTATE LYASE / BETA-ELIMINATION / PECTIN DEGRADATION
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / pectin catabolic process / periplasmic space / metal ion binding
Similarity search - Function
SH3 type barrels. - #880 / Molybdopterin biosynthesis moea protein, domain 2 - #40 / Periplasmic pectate lyase / Periplasmic pectate lyase / Molybdopterin biosynthesis moea protein, domain 2 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / SH3 type barrels. / Roll ...SH3 type barrels. - #880 / Molybdopterin biosynthesis moea protein, domain 2 - #40 / Periplasmic pectate lyase / Periplasmic pectate lyase / Molybdopterin biosynthesis moea protein, domain 2 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Periplasmic pectate lyase
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbbott, D.W. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A Family 2 Pectate Lyase Displays a Rare Fold and Transition Metal-Assisted Beta-Elimination.
Authors: Abbott, D.W. / Boraston, A.B.
History
DepositionAug 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 27, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8042
Polymers61,2571
Non-polymers5461
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.486, 95.642, 126.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PECTATE LYASE /


Mass: 61257.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A1JSS8*PLUS, pectate lyase
#2: Polysaccharide beta-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAb1-4DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112A-1a_1-5][a2112A-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][b-D-GalpA]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENBANK ACCESSION IS CAL14085.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 57.42 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→19.87 Å / Num. obs: 174522 / % possible obs: 94.6 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.87 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rwork0.19 --
obs-174522 94.6 %
Refinement stepCycle: LAST / Resolution: 2.1→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 37 588 4949

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