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- PDB-7xks: Crystal structure of an alkaline pectate lyase from Bacillus clausii -

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Basic information

Entry
Database: PDB / ID: 7xks
TitleCrystal structure of an alkaline pectate lyase from Bacillus clausii
ComponentsPectate lyase
KeywordsLYASE / alkaline pectate
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / polysaccharide catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pectate lyase
Similarity search - Component
Biological speciesAlkalihalobacillus clausii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhou, C. / Zheng, Y.Y. / Liu, W.D. / Ma, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming.
Authors: Zhou, C. / Cao, Y. / Xue, Y. / Liu, W. / Ju, J. / Ma, Y.
History
DepositionApr 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3008
Polymers33,6231
Non-polymers6777
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint7 kcal/mol
Surface area11080 Å2
Unit cell
Length a, b, c (Å)109.085, 109.085, 44.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein Pectate lyase


Mass: 33623.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalihalobacillus clausii (bacteria) / Gene: pelA / Plasmid: PET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0P0J4R7, pectate lyase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05M Mgcl2, 0.1M HEPEs, 30% PEG 550

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 26611 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 21.04 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Χ2: 1.768 / Net I/σ(I): 11.8 / Num. measured all: 276885
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8410.20.85926090.8350.2830.9051.285100
1.84-1.9210.30.62625990.9090.2060.6591.331100
1.92-210.30.40726140.950.1330.4291.417100
2-2.1110.40.30126300.9770.0980.3171.494100
2.11-2.2410.50.21826230.9880.070.2291.629100
2.24-2.4210.60.1726340.9920.0550.1791.76100
2.42-2.6610.70.11726620.9960.0370.1231.635100
2.66-3.0410.70.08226680.9980.0260.0862.06100
3.04-3.8310.40.05327040.9990.0170.0552.52199.9
3.83-309.80.0428680.9990.0130.0422.47999.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMW

3vmw


Resolution: 1.78→27.27 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 1329 5.01 %
Rwork0.1542 25224 -
obs0.1559 26553 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.15 Å2 / Biso mean: 22.5313 Å2 / Biso min: 11.16 Å2
Refinement stepCycle: final / Resolution: 1.78→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 43 172 2568
Biso mean--37.69 33.06 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.78-1.850.23071440.187227352879
1.85-1.940.21381450.169127682913
1.94-2.040.21461460.14727592905
2.04-2.170.19281450.146627522897
2.17-2.330.1651450.139627772922
2.33-2.570.19261480.146527932941
2.57-2.940.18721480.151428082956
2.94-3.70.17761500.151428472997
3.7-27.270.18761580.159929853143

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