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- PDB-1air: PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION ... -

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Basic information

Entry
Database: PDB / ID: 1air
TitlePECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS
ComponentsPECTATE LYASE C
KeywordsPECTATE CLEAVAGE / PECTINOLYITC ACTIVITY / TRANS-ELIMINATION
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 speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsLietzke, S.E. / Scavetta, R.D. / Yoder, M.D. / Jurnak, F.A.
CitationJournal: Plant Physiol. / Year: 1996
Title: The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.
Authors: Lietzke, S.E. / Scavetta, R.D. / Yoder, M.D. / Jurnak, F.
History
DepositionApr 24, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTATE LYASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9263
Polymers37,7341
Non-polymers1922
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.000, 83.000, 95.000
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 C / PELC


Mass: 37733.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Cellular location: EXTRACELLULAR / Plasmid: HB101 / Strain: EC16 / References: UniProt: P11073, pectate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 1.9 M AMMONIUM SULFATE, 0.1M HEPES, PH 7.2 SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: SYMMETRY= (X,Y,Z) SYMMETRY=(-X+1/2,-Y,Z+1/2) SYMMETRY= (-X,Y+1/2,-Z+1/2) ...Details: PROTEIN WAS CRYSTALLIZED FROM 1.9 M AMMONIUM SULFATE, 0.1M HEPES, PH 7.2 SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: SYMMETRY= (X,Y,Z) SYMMETRY=(-X+1/2,-Y,Z+1/2) SYMMETRY= (-X,Y+1/2,-Z+1/2) SYMMETRY=(X+1/2,-Y+1/2,-Z)
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop / Details: Kim, C-Y., (1989) J. Mol. Biol., 208, 365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
225 mMHEPES1drop
320 mM1dropLi2SO4
420 %satpolygalacturonic acid1drop
510 %(w/w)PEG33501drop
6PEG33501reservoir20ml

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 1, 1990 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 25685 / % possible obs: 95.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.175

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Processing

Software
NameVersionClassification
SDMSSOFTWAREdata collection
SDMSSOFTWAREdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -10 %RANDOM
Rwork0.172 ---
obs0.172 25685 96 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 0 128 2770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.774
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.199
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.199

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