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- PDB-6byt: Complex structure of LOR107 mutant (R320) with tetrasaccharide su... -

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Basic information

Entry
Database: PDB / ID: 6byt
TitleComplex structure of LOR107 mutant (R320) with tetrasaccharide substrate
ComponentsShort ulvan lyase
KeywordsLYASE / Complex of LOR107 (R320)
Function / homologyBNR repeat-containing family member / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / Prokaryotic membrane lipoprotein lipid attachment site profile. / lyase activity / extracellular region / metal ion binding / plasma membrane / Ulvan lyase, short isoform
Function and homology information
Biological speciesAlteromonas sp. LOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUlaganathan, T.S. / Cygler, M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.
Authors: Ulaganathan, T. / Helbert, W. / Kopel, M. / Banin, E. / Cygler, M.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short ulvan lyase
B: Short ulvan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,75318
Polymers115,0342
Non-polymers2,71816
Water5,855325
1
A: Short ulvan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7828
Polymers57,5171
Non-polymers1,2657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Short ulvan lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,97010
Polymers57,5171
Non-polymers1,4539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.220, 120.660, 127.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Short ulvan lyase


Mass: 57517.121 Da / Num. of mol.: 2 / Mutation: R320N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas sp. LOR (bacteria) / Gene: LOR_107 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A109PTH9
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 804.657 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2211m-1a_1-5_3*OSO/3=O/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap3SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-L-Rhap3SO3]{[(4+1)][b-D-4-deoxy-GlcpA]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 339 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 25.5% PEG8K, 0.17M Ammonium Sulfate, 0.1M Mes pH 6.5, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→49.05 Å / Num. obs: 66350 / % possible obs: 99.9 % / Redundancy: 5.2 % / Net I/σ(I): 12.93
Reflection shellResolution: 2.2→2.26 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.045 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 3318 5 %
Rwork0.2002 --
obs0.2025 66350 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7627 0 161 325 8113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088010
X-RAY DIFFRACTIONf_angle_d1.02310891
X-RAY DIFFRACTIONf_dihedral_angle_d14.9374545
X-RAY DIFFRACTIONf_chiral_restr0.0841130
X-RAY DIFFRACTIONf_plane_restr0.0061415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23140.3291360.29692599X-RAY DIFFRACTION100
2.2314-2.26470.39451350.28682565X-RAY DIFFRACTION100
2.2647-2.30010.33651360.28552585X-RAY DIFFRACTION100
2.3001-2.33780.31531390.26292624X-RAY DIFFRACTION100
2.3378-2.37810.29951360.25962584X-RAY DIFFRACTION100
2.3781-2.42140.31071360.24972594X-RAY DIFFRACTION100
2.4214-2.4680.29931370.24862599X-RAY DIFFRACTION100
2.468-2.51830.31221360.23592581X-RAY DIFFRACTION100
2.5183-2.57310.29061380.23462622X-RAY DIFFRACTION100
2.5731-2.63290.29991370.24522604X-RAY DIFFRACTION100
2.6329-2.69880.31021370.23482604X-RAY DIFFRACTION100
2.6988-2.77170.27451380.23022617X-RAY DIFFRACTION100
2.7717-2.85330.30891360.23012588X-RAY DIFFRACTION100
2.8533-2.94540.29481380.22882629X-RAY DIFFRACTION100
2.9454-3.05060.30751380.22032612X-RAY DIFFRACTION100
3.0506-3.17280.23461380.20522634X-RAY DIFFRACTION100
3.1728-3.31710.23761370.2012600X-RAY DIFFRACTION100
3.3171-3.4920.24141390.18642646X-RAY DIFFRACTION100
3.492-3.71070.25791390.18262629X-RAY DIFFRACTION100
3.7107-3.99710.20841400.17522657X-RAY DIFFRACTION100
3.9971-4.39910.17081390.14992656X-RAY DIFFRACTION100
4.3991-5.03510.19211410.14372676X-RAY DIFFRACTION100
5.0351-6.34150.20321430.17632707X-RAY DIFFRACTION100
6.3415-49.05710.24571490.21492820X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9205-0.619-1.16431.92660.23322.113-0.3092-0.2274-0.5751-0.0006-0.05260.08740.34410.05420.29330.31770.00770.09680.22710.03590.4083107.69436.5981-15.1145
21.260.0958-0.96350.6949-0.24941.5041-0.08270.03840.01270.0152-0.0215-0.0189-0.0402-0.0480.09910.25150.0215-0.02370.22320.00310.227107.194359.0836-18.3852
31.81470.60311.37392.69160.22982.699-0.44040.230.8989-0.1099-0.0638-0.1332-0.7283-0.05930.38710.56020.0154-0.26080.42630.0680.815966.234982.96599.0637
44.0314-0.25652.04391.70440.12772.8956-0.1138-0.43780.23260.02-0.04810.0051-0.0639-0.43450.11850.2375-0.01350.00080.23570.00430.197172.741360.747619.1889
55.2538-0.25662.53133.7422-0.71652.887-0.239-0.78980.39940.03230.13170.3849-0.0927-0.7860.1190.254-0.0188-0.03730.5361-0.06220.296152.485862.722910.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 263 )
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 520)
3X-RAY DIFFRACTION3chain 'B' and (resid 39 through 247)
4X-RAY DIFFRACTION4chain 'B' and (resid 248 through 422)
5X-RAY DIFFRACTION5chain 'B' and (resid 423 through 520)

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