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- PDB-6hq8: Bacterial beta-1,3-oligosaccharide phosphorylase from GH149 with ... -

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Basic information

Entry
Database: PDB / ID: 6hq8
TitleBacterial beta-1,3-oligosaccharide phosphorylase from GH149 with laminarihexaose bound at a surface site
ComponentsBeta-1,3-oligosaccharide phosphorylase
KeywordsHYDROLASE / Beta-1 / 3-oligosaccharide phosphorylase / Glycosyl hydrolase family 149 / oligosaccharide synthesis / oligosaccharide surface binding site
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsKuhaudomlarp, S. / Stevenson, C.E.M. / Lawson, D.M. / Field, R.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/M02903411 United Kingdom
CitationJournal: Proteins / Year: 2019
Title: The structure of a GH149 beta-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 ...Title: The structure of a GH149 beta-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-beta-(1 → 3)-glucose (laminaribiose) phosphorylase.
Authors: Kuhaudomlarp, S. / Stevenson, C.E.M. / Lawson, D.M. / Field, R.A.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / struct_asym / struct_conn / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-oligosaccharide phosphorylase
B: Beta-1,3-oligosaccharide phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,87123
Polymers268,4252
Non-polymers3,44621
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17210 Å2
ΔGint-32 kcal/mol
Surface area77790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.129, 158.756, 178.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 19 - 1156 / Label seq-ID: 38 - 1175

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-1,3-oligosaccharide phosphorylase


Mass: 134212.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Metagenomic database from Prozomix Ltd / Source: (gene. exp.) metagenome (others) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Transferases; Glycosyltransferases; Hexosyltransferases
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 718 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: Null

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→66.41 Å / Num. obs: 134201 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.037 / Rrim(I) all: 0.138 / Net I/σ(I): 13.5 / Num. measured all: 1808389
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.2913.62.02465120.6370.5692.103100
12.32-66.4111.50.0289380.9990.0090.02998.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6HQ6

6hq6


Resolution: 2.25→66.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.839 / SU ML: 0.159 / SU R Cruickshank DPI: 0.2495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.192
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 6752 5 %RANDOM
Rwork0.1798 ---
obs0.1817 127355 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.25 Å2 / Biso mean: 56.814 Å2 / Biso min: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--1.51 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.25→66.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17973 0 222 730 18925
Biso mean--63.41 47.63 -
Num. residues----2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01418614
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716201
X-RAY DIFFRACTIONr_angle_refined_deg1.211.64825232
X-RAY DIFFRACTIONr_angle_other_deg0.8911.64337860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54152278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98223.959970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.169153058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1361567
X-RAY DIFFRACTIONr_chiral_restr0.060.22478
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023641
Refine LS restraints NCS

Ens-ID: 1 / Number: 37838 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 530 -
Rwork0.278 9234 -
all-9764 -
obs--99.9 %
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)
10.5734-0.13990.04520.7851-0.32260.69490.0072-0.04910.03220.0784-0.0215-0.0048-0.04980.03170.01430.012-0.00550.02190.0067-0.00750.167356.294331.408223.2768
20.60110.1020.29770.4585-0.231.28-0.0209-0.1440.1490.3088-0.0477-0.0906-0.17460.18140.06860.2530.0315-0.05560.15780.04950.410686.70819.570262.4745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 1156
2X-RAY DIFFRACTION2B19 - 1156

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