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- PDB-6hq6: Bacterial beta-1,3-oligosaccharide phosphorylase from GH149 -

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Basic information

Entry
Database: PDB / ID: 6hq6
TitleBacterial beta-1,3-oligosaccharide phosphorylase from GH149
ComponentsBacterial beta-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 / SAD / Resolution: 2.05 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 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)270,33329
Polymers268,4252
Non-polymers1,90827
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-70 kcal/mol
Surface area78630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.239, 158.986, 181.564
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 , 1 types, 2 molecules AB

#1: Protein Bacterial 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

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Non-polymers , 5 types, 892 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
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: 2.05→79.49 Å / Num. obs: 181781 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Net I/σ(I): 14.7 / Num. measured all: 2447545 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.0913.82.38789260.5490.6612.478100
11.23-79.4911.80.02712580.9990.0080.02899.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→79.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.658 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1672 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 9118 5 %RANDOM
Rwork0.182 ---
obs0.1834 172561 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.16 Å2 / Biso mean: 60.281 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 2.05→79.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17810 0 115 901 18826
Biso mean--61.51 48.99 -
Num. residues----2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01418322
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715934
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.64724804
X-RAY DIFFRACTIONr_angle_other_deg0.9061.64737173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52452270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46923.969955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.774153006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5981566
X-RAY DIFFRACTIONr_chiral_restr0.0630.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023606
Refine LS restraints NCS

Ens-ID: 1 / Number: 36910 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 697 -
Rwork0.292 12574 -
all-13271 -
obs--99.88 %
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)
11.0185-0.16870.05310.7226-0.26460.5550.0425-0.2358-0.04180.0337-0.0290.0225-0.02380.0091-0.01350.1356-0.02420.02680.06250.0030.023756.857532.189723.4646
21.04990.26550.20480.7961-0.2930.99540.0891-0.6112-0.02020.4274-0.1667-0.1146-0.19380.18750.07760.4313-0.0623-0.03110.56750.16350.243687.737221.036161.9599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 1156
2X-RAY DIFFRACTION2B19 - 1156

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