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- PDB-4l22: Crystal structure of putative glycogen phosphorylase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 4l22
TitleCrystal structure of putative glycogen phosphorylase from Streptococcus mutans
ComponentsPhosphorylase
KeywordsTRANSFERASE / glycogen phosphorylase activity
Function / homology
Function and homology information


maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLihan, M.-Y. / Li, G.-L. / Li, L.-F. / Su, X.-D.
CitationJournal: To be Published
Title: Crystal structure of putative glycogen phosphorylase from Streptococcus mutans
Authors: Lihan, M.-Y. / Li, G.-L. / Li, L.-F. / Su, X.-D.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphorylase


Theoretical massNumber of molelcules
Total (without water)86,9211
Polymers86,9211
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.720, 85.020, 84.460
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphorylase


Mass: 86920.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 700610 / UA159 / Gene: glgP, SMU_1564 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DT31, glycogen phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 289 K / Method: solid-liquid interface method / pH: 8.5
Details: 0.2M (NH4)2SO4, 0.1M Tris, 25% PEG3350, pH 8.5, Solid-liquid interface method, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979142 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979142 Å / Relative weight: 1
ReflectionResolution: 2.45→84.32 Å / Num. obs: 38983

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C4M

2c4m


Resolution: 2.45→84.32 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.705 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 1.061 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26597 1402 5.1 %RANDOM
Rwork0.2216 ---
obs0.22385 26253 88.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å23.69 Å2
2--0.39 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.45→84.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 0 28 6114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196204
X-RAY DIFFRACTIONr_bond_other_d0.0010.025974
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9638390
X-RAY DIFFRACTIONr_angle_other_deg0.72313761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021394
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_it3.2675.1943011
X-RAY DIFFRACTIONr_mcbond_other3.2665.1933010
X-RAY DIFFRACTIONr_mcangle_it4.7437.7943762
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5015.4773193
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 65 -
Rwork0.378 1521 -
obs--69.23 %

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