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- PDB-2qx3: Structure of pectate lyase II from Xanthomonas campestris pv. cam... -

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Basic information

Entry
Database: PDB / ID: 2qx3
TitleStructure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913
ComponentsPectate lyase II
KeywordsLYASE / parallel beta helix
Function / homology
Function and homology information


pectate lyase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Pectin lyase family / Pectate lyase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Pectate lyase II
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarron, M.L. / Shaya, D.
CitationJournal: To be Published
Title: A seductive method to improve the thermostability and activity of an enzyme
Authors: Lau, P.C. / Xiao, Z.Z. / Sulea, T. / Bergeron, H. / Grosse, S. / Beauchemin, M.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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 II
B: Pectate lyase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0257
Polymers70,5502
Non-polymers4755
Water10,773598
1
A: Pectate lyase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4653
Polymers35,2751
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pectate lyase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5604
Polymers35,2751
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.183, 53.158, 73.057
Angle α, β, γ (deg.)71.720, 80.030, 69.100
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pectate lyase II /


Mass: 35275.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: ATCC 33913 / Gene: pelB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P6Z9, pectate lyase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes, 25% polyethylene glycol 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 20.1 / Number: 66970 / Rmerge(I) obs: 0.058 / Χ2: 3.02 / D res high: 2 Å / D res low: 25 Å / Num. obs: 35612 / % possible obs: 83.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.3259810.0271.9711.9
3.424.396.810.0433.381.9
2.993.4292.710.0654.6691.9
2.712.999210.0844.2171.9
2.522.7192.310.0993.2891.9
2.372.5292.510.1092.8051.9
2.252.3792.610.1262.5141.9
2.152.2585.910.1442.2291.9
2.072.1556.310.1762.0831.8
22.0737.210.211.7291.7
ReflectionResolution: 2→25 Å / Num. all: 35612 / Num. obs: 35612 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.058 / Χ2: 3.024 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.071.70.2115841.72937.2
2.07-2.151.80.17624152.08356.3
2.15-2.251.90.14436472.22985.9
2.25-2.371.90.12639542.51492.6
2.37-2.521.90.10939472.80592.5
2.52-2.711.90.09939053.28992.3
2.71-2.991.90.08439224.21792
2.99-3.421.90.06539414.66992.7
3.42-4.31.90.04341353.3896.8
4.3-251.90.02741621.97198

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.33 Å24.58 Å
Translation2.33 Å24.58 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIR

1air


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.088 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1785 5 %RANDOM
Rwork0.157 ---
obs0.16 35612 83.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20.46 Å20.08 Å2
2---0.19 Å2-0.38 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5181 0 25 598 5804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225349
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.937312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41725.417240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58815846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0821516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024176
X-RAY DIFFRACTIONr_nbd_refined0.190.22766
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2578
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.226
X-RAY DIFFRACTIONr_mcbond_it0.4111.53467
X-RAY DIFFRACTIONr_mcangle_it0.71725480
X-RAY DIFFRACTIONr_scbond_it1.19532154
X-RAY DIFFRACTIONr_scangle_it1.8184.51823
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 43 -
Rwork0.242 1013 -
obs-1056 32.91 %

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