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- PDB-5gt5: Structural basis of the specific activity and thermostability of ... -

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Basic information

Entry
Database: PDB / ID: 5gt5
TitleStructural basis of the specific activity and thermostability of pectate lyase (pelN) from Paenibacillus sp. 0602
ComponentsPectate lyase
KeywordsLYASE / pectate lyase / Paenibacillus sp. 0602
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesPaenibacillus sp. 0602 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsZhou, Z.P. / Liu, Y. / Song, J.N.
Funding support China, 1items
OrganizationGrant numberCountry
the Knowledge Innovation Program of CASKSCX2-EW-G-8 China
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.
Authors: Zhou, Z. / Liu, Y. / Chang, Z. / Wang, H. / Leier, A. / Marquez-Lago, T.T. / Ma, Y. / Li, J. / Song, J.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase
B: Pectate lyase


Theoretical massNumber of molelcules
Total (without water)96,5472
Polymers96,5472
Non-polymers00
Water26,3921465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.552, 55.584, 83.182
Angle α, β, γ (deg.)74.26, 84.40, 73.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pectate lyase


Mass: 48273.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. 0602 (bacteria) / Gene: pelN / Production host: Escherichia coli (E. coli) / References: UniProt: W8CR80, pectate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1465 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3000, 100mM Na2HPO4 / PH range: 4.0-4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 629583 / % possible obs: 99.8 % / Redundancy: 7.4 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSC

3zsc


Resolution: 1.449→34.431 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 7021 4.89 %
Rwork0.1495 --
obs0.1507 143651 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.449→34.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 0 1467 8233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116932
X-RAY DIFFRACTIONf_angle_d1.3749410
X-RAY DIFFRACTIONf_dihedral_angle_d11.1672472
X-RAY DIFFRACTIONf_chiral_restr0.0921046
X-RAY DIFFRACTIONf_plane_restr0.0071216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4493-1.46580.25522240.21193842X-RAY DIFFRACTION78
1.4658-1.4830.23152110.19724161X-RAY DIFFRACTION83
1.483-1.50110.23252190.19394170X-RAY DIFFRACTION85
1.5011-1.52010.21252280.18054186X-RAY DIFFRACTION85
1.5201-1.54010.22252190.16994349X-RAY DIFFRACTION86
1.5401-1.56120.20812300.16074342X-RAY DIFFRACTION88
1.5612-1.58350.18462330.16394402X-RAY DIFFRACTION88
1.5835-1.60720.19782100.16034429X-RAY DIFFRACTION89
1.6072-1.63230.21082340.16224507X-RAY DIFFRACTION89
1.6323-1.6590.19372070.1534367X-RAY DIFFRACTION88
1.659-1.68760.18882190.15584500X-RAY DIFFRACTION90
1.6876-1.71830.19532410.15474526X-RAY DIFFRACTION91
1.7183-1.75140.19482140.15624521X-RAY DIFFRACTION91
1.7514-1.78710.18832400.15644581X-RAY DIFFRACTION92
1.7871-1.8260.17662500.15084514X-RAY DIFFRACTION92
1.826-1.86850.16892330.14654649X-RAY DIFFRACTION93
1.8685-1.91520.16452430.14114686X-RAY DIFFRACTION93
1.9152-1.9670.1542310.14194662X-RAY DIFFRACTION94
1.967-2.02480.17092450.14474672X-RAY DIFFRACTION94
2.0248-2.09020.17552190.14724764X-RAY DIFFRACTION95
2.0902-2.16490.1912250.14314755X-RAY DIFFRACTION95
2.1649-2.25150.15392620.14134786X-RAY DIFFRACTION96
2.2515-2.3540.16232370.14464760X-RAY DIFFRACTION96
2.354-2.47810.19332300.15514794X-RAY DIFFRACTION96
2.4781-2.63330.18692660.15474773X-RAY DIFFRACTION96
2.6333-2.83650.17242270.15834755X-RAY DIFFRACTION96
2.8365-3.12180.17892330.15234798X-RAY DIFFRACTION95
3.1218-3.57310.14952740.14314594X-RAY DIFFRACTION93
3.5731-4.50010.13752680.12434923X-RAY DIFFRACTION99
4.5001-34.44050.15322490.14774862X-RAY DIFFRACTION97

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