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- PDB-5h42: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lach... -

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Basic information

Entry
Database: PDB / ID: 5h42
TitleCrystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate
ComponentsUncharacterized protein
KeywordsTRANSFERASE / beta-1 / 2-glucan / glycoside phosphorylase
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / : / : / Glycoside phosphorylase supersandwich domain / Glycoside phosphorylase C-terminal domain / SOGP N-terminal domain / : / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycosyltransferase - #10 ...: / : / : / Glycoside phosphorylase supersandwich domain / Glycoside phosphorylase C-terminal domain / SOGP N-terminal domain / : / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
1-O-phosphono-alpha-D-glucopyranose / alpha-D-glucopyranose / Uncharacterized protein
Similarity search - Component
Biological speciesClostridium phytofermentans ISDg (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakajima, M. / Tanaka, N. / Furukawa, N. / Nihira, T. / Kodutsumi, Y. / Takahashi, Y. / Sugimoto, N. / Miyanaga, A. / Fushinobu, S. / Taguchi, H. / Nakai, H.
CitationJournal: Sci Rep / Year: 2017
Title: Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Authors: Nakajima, M. / Tanaka, N. / Furukawa, N. / Nihira, T. / Kodutsumi, Y. / Takahashi, Y. / Sugimoto, N. / Miyanaga, A. / Fushinobu, S. / Taguchi, H. / Nakai, H.
History
DepositionOct 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
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 1.3Nov 8, 2023Group: 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,1426
Polymers255,1812
Non-polymers9614
Water11,746652
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8512
Polymers127,5911
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2914
Polymers127,5911
Non-polymers7003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.469, 94.778, 156.851
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 1113 / Label seq-ID: 2 - 1114

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

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Components

#1: Protein Uncharacterized protein / 1 / 2-beta-oligoglucan phosphorylase


Mass: 127590.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans ISDg (bacteria)
Strain: ISDg / Gene: Cphy_0694 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9KJS6, EC: 2.4.1.333
#2: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, calcium acetate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 141346 / % possible obs: 96 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 9.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 25837 / Num. unique all: 6983 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H3Z

5h3z


Resolution: 2.1→48.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.864 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 6950 4.9 %RANDOM
Rwork0.19466 ---
obs0.19666 134392 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.596 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17800 0 60 652 18512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01918308
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216974
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.94824873
X-RAY DIFFRACTIONr_angle_other_deg1.309339066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96552218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45624.456891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.424153028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4391578
X-RAY DIFFRACTIONr_chiral_restr0.1010.22736
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0220827
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024395
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_it1.8362.4288881
X-RAY DIFFRACTIONr_mcbond_other1.8362.4288880
X-RAY DIFFRACTIONr_mcangle_it2.6843.63611096
X-RAY DIFFRACTIONr_mcangle_other2.6843.63711097
X-RAY DIFFRACTIONr_scbond_it2.5162.6719427
X-RAY DIFFRACTIONr_scbond_other2.5162.6719427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8773.91213778
X-RAY DIFFRACTIONr_long_range_B_refined5.12519.47820910
X-RAY DIFFRACTIONr_long_range_B_other5.10519.46820725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 143064 / 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: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 538 -
Rwork0.256 9382 -
obs--91.38 %

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