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- PDB-5olq: Rhamnogalacturonan lyase -

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Basic information

Entry
Database: PDB / ID: 5olq
TitleRhamnogalacturonan lyase
ComponentsRhamnogalacturonan lyase
KeywordsLYASE / Pectin / PL9 / polysaccharide lyase family 9 / Rhamnogalacturonan lyase / endo-acting enzyme
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / alpha-galactosidase activity / extracellular region / metal ion binding
Similarity search - Function
Domain of unknown function DUF4990 / Rhamnogalacturonan lyase BT_4170-like, C-terminal / : / Pel9A-like, right handed beta helix region / : / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
PHOSPHATE ION / DUF4990 domain-containing protein / Pectate lyase L
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBasle, A. / Luis, A.S. / Gilbert, H.J.
CitationJournal: Nat Microbiol / Year: 2018
Title: Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.
Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / ...Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / Venditto, I. / Ralet, M.C. / Henrissat, B. / Martens, E.C. / Mosimann, S.C. / Abbott, D.W. / Gilbert, H.J.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnogalacturonan lyase
B: Rhamnogalacturonan lyase
C: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,3469
Polymers170,9413
Non-polymers4056
Water27,3651519
1
A: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1153
Polymers56,9801
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1153
Polymers56,9801
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rhamnogalacturonan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1153
Polymers56,9801
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.550, 123.820, 138.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rhamnogalacturonan lyase


Mass: 56980.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: HMPREF2534_01516 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139KMS2, UniProt: Q8A051*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1519 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM sodium/potassium phosphate 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.48→39.65 Å / Num. obs: 221195 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 13.4
Reflection shellResolution: 1.48→1.51 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 10868 / CC1/2: 0.736 / % possible all: 99.9

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Processing

Software
NameClassification
xia2data reduction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU4

1ru4


Resolution: 1.48→39.65 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.218 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 10869 4.9 %RANDOM
Rwork0.12676 ---
obs0.12883 210226 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.48 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.48→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9800 0 18 1519 11337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910145
X-RAY DIFFRACTIONr_bond_other_d0.0020.028912
X-RAY DIFFRACTIONr_angle_refined_deg1.541.93913763
X-RAY DIFFRACTIONr_angle_other_deg0.986320795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12151306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52124.919496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.414151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3791544
X-RAY DIFFRACTIONr_chiral_restr0.0980.21457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022083
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4491.3945143
X-RAY DIFFRACTIONr_mcbond_other1.4481.3935142
X-RAY DIFFRACTIONr_mcangle_it1.8342.1026431
X-RAY DIFFRACTIONr_mcangle_other1.8342.1026432
X-RAY DIFFRACTIONr_scbond_it2.1031.6255002
X-RAY DIFFRACTIONr_scbond_other2.0911.6234991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4542.3427300
X-RAY DIFFRACTIONr_long_range_B_refined3.09318.31311314
X-RAY DIFFRACTIONr_long_range_B_other2.82817.45510928
X-RAY DIFFRACTIONr_rigid_bond_restr1.851319057
X-RAY DIFFRACTIONr_sphericity_free22.37651040
X-RAY DIFFRACTIONr_sphericity_bonded7.368519300
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 810 -
Rwork0.172 15436 -
obs--99.91 %

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