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- PDB-6f2p: Structure of Paenibacillus xanthan lyase to 2.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 6f2p
TitleStructure of Paenibacillus xanthan lyase to 2.6 A resolution
ComponentsPaenibacillus xanthan lyase
KeywordsLYASE / lyase enzyme xanthan
Function / homology
Function and homology information


xanthan lyase / xanthan lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
CBM6/CBM35/CBM36-like 2 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase ...CBM6/CBM35/CBM36-like 2 / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Paenibacillus xanthan lyase
Similarity search - Component
Biological speciesPaenibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLo Leggio, L. / Kadziola, A.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity.
Authors: Jensen, P.F. / Kadziola, A. / Comamala, G. / Segura, D.R. / Anderson, L. / Poulsen, J.N. / Rasmussen, K.K. / Agarwal, S. / Sainathan, R.K. / Monrad, R.N. / Svendsen, A. / Nielsen, J.E. / Lo ...Authors: Jensen, P.F. / Kadziola, A. / Comamala, G. / Segura, D.R. / Anderson, L. / Poulsen, J.N. / Rasmussen, K.K. / Agarwal, S. / Sainathan, R.K. / Monrad, R.N. / Svendsen, A. / Nielsen, J.E. / Lo Leggio, L. / Rand, K.D.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paenibacillus xanthan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,99642
Polymers113,0931
Non-polymers3,90241
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-126 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.610, 100.610, 324.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Paenibacillus xanthan lyase


Mass: 113093.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A493R6T1*PLUS, xanthan lyase

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Non-polymers , 6 types, 556 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 4 mg/mL. Reservoir: 0.2 M CaCl2, 0.1 M Bis-Tris pH5.5, 45 %v/v MPD. 100 uL Drop: 75 % protein 25 % reservour. 0.3 uL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.053 Å / Num. obs: 51793 / % possible obs: 98.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.208 / Net I/σ(I): 11.43
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 3728 / CC1/2: 0.687 / Rrim(I) all: 1.388 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+24 / Resolution: 2.6→48.053 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2129 1999 3.86 %
Rwork0.1651 --
obs0.167 51722 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7964 0 243 515 8722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068372
X-RAY DIFFRACTIONf_angle_d0.9911415
X-RAY DIFFRACTIONf_dihedral_angle_d14.2552973
X-RAY DIFFRACTIONf_chiral_restr0.0761269
X-RAY DIFFRACTIONf_plane_restr0.0041436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.30061380.26863447X-RAY DIFFRACTION98
2.665-2.73710.34451400.24813475X-RAY DIFFRACTION98
2.7371-2.81760.27541380.23473460X-RAY DIFFRACTION98
2.8176-2.90860.27971400.21733471X-RAY DIFFRACTION98
2.9086-3.01250.27781400.20843489X-RAY DIFFRACTION98
3.0125-3.13310.22871420.19823505X-RAY DIFFRACTION99
3.1331-3.27570.23831390.18143495X-RAY DIFFRACTION98
3.2757-3.44830.22511420.1623531X-RAY DIFFRACTION99
3.4483-3.66430.19821430.15013554X-RAY DIFFRACTION99
3.6643-3.94710.21491440.13833566X-RAY DIFFRACTION99
3.9471-4.34410.1741430.12273565X-RAY DIFFRACTION99
4.3441-4.97210.16171460.11683629X-RAY DIFFRACTION99
4.9721-6.26210.19431480.15883678X-RAY DIFFRACTION99
6.2621-48.0610.17321560.16183858X-RAY DIFFRACTION99

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