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- PDB-6gh2: Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-glc-... -

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Basic information

Entry
Database: PDB / ID: 6gh2
TitlePaenibacillus sp. YM1 laminaribiose phosphorylase with alpha-glc-1-phosphate bound
ComponentsLaminaribiose phosphorylase
KeywordsHYDROLASE / laminaribiose phosphorylase / Glycosyl hydrolase 94 / disaccharide synthesis / CARBOHYDRATE
Function / homology
Function and homology information


laminaribiose phosphorylase / laminaribiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
1-O-phosphono-alpha-D-glucopyranose / Laminaribiose phosphorylase
Similarity search - Component
Biological speciesPaenibacillus sp. YM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsKuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P010660/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/M02903411 United Kingdom
CitationJournal: Chembiochem / Year: 2019
Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation ...Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy.
Authors: Kuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / 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_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_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: Laminaribiose phosphorylase
B: Laminaribiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,02317
Polymers203,7352
Non-polymers1,28915
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-46 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.405, 146.405, 221.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 4 - 907 / Label seq-ID: 6 - 909

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 Laminaribiose phosphorylase


Mass: 101867.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Two residues with sequence Gly-Pro are appended to the N-terminus which are left over after cleavage of the tag
Source: (gene. exp.) Paenibacillus sp. YM1 (bacteria) / Gene: lbpA / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7UT17, laminaribiose phosphorylase
#3: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 574 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / 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.: 561 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Null

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→75.69 Å / Num. obs: 83874 / % possible obs: 100 % / Redundancy: 17.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.051 / Rrim(I) all: 0.223 / Net I/σ(I): 13.6 / Num. measured all: 1492934 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.5518.21.80945290.6240.4241.859100
12.99-75.6914.80.03572510.0090.03699.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GGY

6ggy


Resolution: 2.5→75.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.874 / SU ML: 0.188 / SU R Cruickshank DPI: 0.3827 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4278 5.1 %RANDOM
Rwork0.1794 ---
obs0.1813 79503 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.13 Å2 / Biso mean: 48.387 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.84 Å2
Refinement stepCycle: final / Resolution: 2.5→75.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13965 0 74 580 14619
Biso mean--50.72 37.53 -
Num. residues----1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914404
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212854
X-RAY DIFFRACTIONr_angle_refined_deg1.341.94819559
X-RAY DIFFRACTIONr_angle_other_deg0.943329602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34151823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84823.411689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.646152193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.40415112
X-RAY DIFFRACTIONr_chiral_restr0.0750.22095
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023197
Refine LS restraints NCS

Ens-ID: 1 / Number: 58824 / 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: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 288 -
Rwork0.26 5815 -
all-6103 -
obs--99.84 %
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)
10.9264-0.2025-0.12290.43120.20282.4522-0.17020.1424-0.15660.1114-0.0890.03610.7231-0.35890.25920.3316-0.16350.17280.0878-0.08120.126149.874-1.306453.7186
23.126-2.48961.5832.0357-1.441.657-0.4193-0.02370.06290.38510.1656-0.0297-0.1698-0.89210.25370.2077-0.22710.18651.1238-0.43170.344228.571617.384639.2305
31.1855-0.18590.10991.2921-0.18611.39380.00650.04190.0921-0.032-0.28170.37870.0313-0.77160.27520.0244-0.03460.00790.6385-0.26660.214730.102118.423822.7354
41.1309-2.1137-2.17875.08775.18265.31650.3579-0.0930.2652-0.3647-0.46020.2386-0.3007-0.54690.10230.5596-0.43550.04370.9319-0.14270.763418.879-8.535616.2071
50.8585-0.052-0.18550.85440.38522.046-0.0867-0.0249-0.02140.05040.0229-0.06690.06570.22820.06390.0281-0.00960.01250.05410.01930.062973.575322.568151.0213
65.46040.9274-0.65793.5901-0.3993.16580.01950.65810.0106-0.34580.14670.1369-0.2933-0.2139-0.16620.35410.02620.05420.08840.02730.12351.921349.308468.0623
71.2905-0.2891-0.75781.14040.05071.46390.0629-0.08260.22080.15650.01610.0216-0.38250.0765-0.0790.2298-0.02470.00960.0146-0.00390.087254.817940.939983.4594
83.2815-1.96612.92076.9135-1.75782.6222-0.3752-0.19710.30460.39410.2015-0.1309-0.3775-0.07980.17380.5211-0.28180.00260.6348-0.13460.580982.599153.46286.5302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 359
2X-RAY DIFFRACTION2A360 - 430
3X-RAY DIFFRACTION3A431 - 872
4X-RAY DIFFRACTION4A873 - 911
5X-RAY DIFFRACTION5B4 - 370
6X-RAY DIFFRACTION6B371 - 482
7X-RAY DIFFRACTION7B483 - 865
8X-RAY DIFFRACTION8B866 - 908

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