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- PDB-1zcv: apo form of a mutant of glycogenin in which Asp159 is replaced by Asn -

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Basic information

Entry
Database: PDB / ID: 1zcv
Titleapo form of a mutant of glycogenin in which Asp159 is replaced by Asn
ComponentsGlycogenin-1
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHurley, T.D. / Stout, S.L. / Miner, E. / Zhou, J. / Roach, P.J.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Requirements for catalysis in mammalian glycogenin.
Authors: Hurley, T.D. / Stout, S. / Miner, E. / Zhou, J. / Roach, P.J.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: The structure of the autocatalytic initiator of glycogen synthesis, glycogenin
Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D.
History
DepositionApr 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6992
Polymers39,6031
Non-polymers961
Water3,117173
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3994
Polymers79,2062
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2540 Å2
ΔGint-26 kcal/mol
Surface area22520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.030, 105.780, 122.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-427-

HOH

31A-521-

HOH

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Components

#1: Protein Glycogenin-1


Mass: 39603.219 Da / Num. of mol.: 1 / Mutation: D159N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GYG, GYG1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: P13280, glycogenin glucosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: sodium MES, PEG MME 5000, ammonium sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2004
RadiationMonochromator: APS 17ID design / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 27057 / Num. obs: 26783 / % possible obs: 99.3 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 6.9 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.034 / Χ2: 0.978 / Net I/σ(I): 49.5
Reflection shellResolution: 1.98→2.05 Å / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.178 / Num. measured obs: 2625 / Χ2: 0.897 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LL3

1ll3


Resolution: 1.98→29.5 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1306 4.8 %random
Rwork0.209 ---
all0.242 27057 --
obs0.21 26170 96.7 %-
Solvent computationBsol: 33.368 Å2
Displacement parametersBiso mean: 34.816 Å2
Baniso -1Baniso -2Baniso -3
1--4.722 Å20 Å20 Å2
2--1.919 Å20 Å2
3---2.803 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.98→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 2 173 2238
Refine LS restraints
Refine-IDTypeDev idealWeightDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4681.5
X-RAY DIFFRACTIONc_scbond_it2.120
X-RAY DIFFRACTIONc_mcangle_it2.39620
X-RAY DIFFRACTIONc_scangle_it3.1662.50
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.17
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.07
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4sso.param

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