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- PDB-1jta: Crystal Structure of Pectate Lyase A (C2 form) -

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Basic information

Entry
Database: PDB / ID: 1jta
TitleCrystal Structure of Pectate Lyase A (C2 form)
Componentspectate lyase A
KeywordsLYASE / parallel beta helix beta-elimination mechanism
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThomas, L.M. / Doan, C.N. / 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 20, 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 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 1.4Oct 16, 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8912
Polymers38,7951
Non-polymers961
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.549, 53.802, 71.039
Angle α, β, γ (deg.)90.00, 109.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein pectate lyase A


Mass: 38794.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: EC16 / Gene: pelA / Plasmid: pel812 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Lithium sulfate, PEG 8K, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Doan, C.N., (2000) Acta Crystallogr., D56, 351.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 %(w/v)PEG80001drop
26 %PEG10001drop
35 mMHEPES1droppH7.0
412 %PEG80001reservoir
512 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→31.68 Å / Num. all: 29056 / Num. obs: 26888 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.041
Reflection shellResolution: 1.8→1.88 Å / Num. unique all: 4111 / % possible all: 94.4
Reflection
*PLUS
Num. obs: 36568 / % possible obs: 88.3 % / Num. measured all: 88736 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 64.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6.28

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PelE from Erwinia chrysanthemi EC16

Resolution: 1.8→31.68 Å / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2667 -random
Rwork0.181 ---
obs0.181 26888 92.5 %-
all-29056 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.056 Å20 Å21.418 Å2
2---1.676 Å20 Å2
3---1.732 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.8→31.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 5 244 2967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.075
X-RAY DIFFRACTIONc_mcangle_it1.539
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.615
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.2318 318 -
Rwork0.1766 --
obs--94.4 %
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.2253 / Rfactor Rwork: 0.1815
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.401
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.482
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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