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- PDB-2v8i: Structure of a Family 2 Pectate Lyase in a Native Form -

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Basic information

Entry
Database: PDB / ID: 2v8i
TitleStructure of a Family 2 Pectate Lyase in a Native Form
ComponentsPECTATE LYASE
KeywordsLYASE / PERIPLASM / 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
IODIDE ION / Periplasmic pectate lyase
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.5 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 -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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)67,73052
Polymers61,2571
Non-polymers6,47251
Water13,673759
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: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.44 Å3/Da / Density % sol: 57.42 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5148
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionResolution: 1.5→19.59 Å / Num. obs: 105592 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.5→19.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.627 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 5574 5 %RANDOM
Rwork0.222 ---
obs0.223 105592 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 51 759 5134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9576064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63724.138232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45315742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0871532
X-RAY DIFFRACTIONr_chiral_restr0.0760.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23081
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2662
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.52786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0824342
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.70631933
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6744.51719
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.533 388
Rwork0.483 7173

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