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- PDB-1jrg: Crystal Structure of the R3 form of Pectate Lyase A, Erwinia chry... -

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Basic information

Entry
Database: PDB / ID: 1jrg
TitleCrystal Structure of the R3 form of Pectate Lyase A, Erwinia chrysanthemi
ComponentsPectate lyase
KeywordsLYASE / parallel beta helix beta 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
Pectate lyase A / Pectate lyase A
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThomas, L.M. / Doan, C. / Oliver, R.L. / Yoder, M.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of pectate lyase A: comparison to other isoforms.
Authors: Thomas, L.M. / Doan, C.N. / Oliver, R.L. / Yoder, M.D.
History
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9736
Polymers77,5892
Non-polymers3844
Water5,873326
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9873
Polymers38,7951
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9873
Polymers38,7951
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.055, 98.055, 217.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Pectate lyase


Mass: 38794.609 Da / Num. of mol.: 2 / Fragment: Pectate lyase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: EC16 / Gene: PELA / Plasmid: pPEL812 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P29155, UniProt: P0C1A2*PLUS, pectate lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, PEG1K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.0
20.5 M1dropLi2SO4
31 %PEG80001drop
41 M1reservoirLi2SO4
52 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 45453 / Num. obs: 41984 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.077 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.31 / % possible all: 99
Reflection
*PLUS
Num. obs: 44138 / % possible obs: 98.3 % / Num. measured all: 111710 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PelE search model comprised of residues 30-61, 70-100, 105-251, 258-280, 293-314, and 323-332. (Coordinates provided by F. Jurnak)

Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3990 -random
Rwork0.16 ---
obs0.16 41984 92.4 %-
all-45453 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.216 Å2-1.56 Å20 Å2
2---1.216 Å20 Å2
3---2.432 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 20 326 5655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.424
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_mcbond_it1.057
X-RAY DIFFRACTIONc_mcangle_it1.753
X-RAY DIFFRACTIONc_scbond_it1.526
X-RAY DIFFRACTIONc_scangle_it2.175
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.261 406
Rwork0.2207 4105
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rfree: 0.2109 / Rfactor Rwork: 0.1596
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.418
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.001
LS refinement shell
*PLUS
Rfactor Rfree: 0.261

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