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- PDB-3b90: Crystal Structure of the Catalytic Domain of Pectate Lyase PelI f... -

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Basic information

Entry
Database: PDB / ID: 3b90
TitleCrystal Structure of the Catalytic Domain of Pectate Lyase PelI from Erwinia chrysanthemi
ComponentsEndo-pectate lyase
KeywordsLYASE / Pectate Lyase / Pectin / Galacturonic Acid / Erwinia chrysanthemi / right-handed parallel beta helix fold / catalytic domain
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCreze, C. / Castang, S. / Derivery, E. / Haser, R. / Shevchik, V. / Gouet, P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of Pectate Lyase PelI from Soft Rot Pathogen Erwinia chrysanthemi in Complex with Its Substrate
Authors: Creze, C. / Castang, S. / Derivery, E. / Haser, R. / Hugouvieux-Cotte-Pattat, N. / Shevchik, V.E. / Gouet, P.
History
DepositionNov 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-pectate lyase
B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water5,855325
1
A: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1195
Polymers23,8521
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1195
Polymers23,8521
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Endo-pectate lyase
hetero molecules

A: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2500 Å2
ΔGint-192 kcal/mol
Surface area17890 Å2
MethodPISA
4
A: Endo-pectate lyase
hetero molecules

B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area2260 Å2
ΔGint-183 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 62.600, 128.100
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 Endo-pectate lyase


Mass: 23851.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: pelI / Plasmid: pT7-6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O50325, pectate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT AT THIS POSITION IT IS INDEED ARG171 AND THE DATABASE IS INCORRECT.

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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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M zinc sulfate heptahydrate, 0.1 M MES, 25% PEG 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 21791 / Num. obs: 20021 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2172 / Rsym value: 0.186 / % possible all: 77.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→19.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1891203.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 974 4.9 %RANDOM
Rwork0.21 ---
obs0.21 20020 91.9 %-
all-21785 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7373 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å20 Å20 Å2
2--9.68 Å20 Å2
3----5.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.11→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 16 325 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 2.11→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 130 4.8 %
Rwork0.217 2575 -
obs-2600 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2SO4.parSO4.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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