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- PDB-5h3z: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lach... -

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Basic information

Entry
Database: PDB / ID: 5h3z
TitleCrystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
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
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesClostridium phytofermentans ISDg (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)258,32318
Polymers256,9632
Non-polymers1,36016
Water15,691871
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1028
Polymers128,4821
Non-polymers6217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,22010
Polymers128,4821
Non-polymers7399
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-8 kcal/mol
Surface area73660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.761, 94.784, 157.943
Angle α, β, γ (deg.)90.00, 98.41, 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: 128481.602 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 (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A9KJS6, EC: 2.4.1.333
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris-HCl, calcium acetate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 172867 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 25.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2.8 / Num. unique all: 8557 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→42.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.04 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20359 8658 5 %RANDOM
Rwork0.16842 ---
obs0.17019 164157 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17836 0 84 871 18791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01918363
X-RAY DIFFRACTIONr_bond_other_d0.0080.0217076
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.95424918
X-RAY DIFFRACTIONr_angle_other_deg1.371339293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48952226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88924.462892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.291152924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031578
X-RAY DIFFRACTIONr_chiral_restr0.1130.22735
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0220888
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024402
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_it2.5872.9118907
X-RAY DIFFRACTIONr_mcbond_other2.5872.9118906
X-RAY DIFFRACTIONr_mcangle_it3.394.35211132
X-RAY DIFFRACTIONr_mcangle_other3.394.35311133
X-RAY DIFFRACTIONr_scbond_it3.5143.2289456
X-RAY DIFFRACTIONr_scbond_other3.5143.2289456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0584.70513787
X-RAY DIFFRACTIONr_long_range_B_refined6.03123.68621027
X-RAY DIFFRACTIONr_long_range_B_other6.0323.60720730
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 141736 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 566 -
Rwork0.247 11528 -
obs--95.19 %

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