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- PDB-1rzv: Crystal structure of the glycogen synthase from Agrobacterium tum... -

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Basic information

Entry
Database: PDB / ID: 1rzv
TitleCrystal structure of the glycogen synthase from Agrobacterium tumefaciens (non-complexed form)
ComponentsGlycogen synthase 1
KeywordsTRANSFERASE / glycosyl-transferase GT-B fold / Rossmann fold
Function / homology
Function and homology information


starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / glycogen (starch) synthase activity / glycogen biosynthetic process / cytosol
Similarity search - Function
Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBuschiazzo, A. / Guerin, M.E. / Ugalde, J.E. / Ugalde, R.A. / Shepard, W. / Alzari, P.M.
Citation
Journal: Embo J. / Year: 2004
Title: Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation.
Authors: Buschiazzo, A. / Ugalde, J.E. / Guerin, M.E. / Shepard, W. / Ugalde, R.A. / Alzari, P.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary crystallographic studies of glycogen synthase from Agrobacterium tumefaciens
Authors: Guerin, M.E. / Buschiazzo, A. / Ugalde, J.E. / Ugalde, R.A. / Alzari, P.M.
History
DepositionDec 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen synthase 1
B: Glycogen synthase 1


Theoretical massNumber of molelcules
Total (without water)105,8512
Polymers105,8512
Non-polymers00
Water7,332407
1
A: Glycogen synthase 1


Theoretical massNumber of molelcules
Total (without water)52,9261
Polymers52,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase 1


Theoretical massNumber of molelcules
Total (without water)52,9261
Polymers52,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.271, 87.289, 88.492
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycogen synthase 1 / Starch [bacterial glycogen] synthase 1


Mass: 52925.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: GLGA1, GLGA, ATU4075, AGR_L_1562 / Plasmid: pBBRMCS-4 / Production host: Agrobacterium tumefaciens (bacteria) / Strain (production host): A5130
References: UniProt: P0A3F3, starch synthase (glycosyl-transferring)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.6 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2002
Details: channel - cut Si monochromator + cylindrical grazing incidence mirror
RadiationMonochromator: channel cut Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→29.97 Å / Num. all: 88607 / Num. obs: 88607 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 37 / Limit k min: 0 / Limit l max: 37 / Limit l min: -38 / Observed criterion F max: 1545415.8 / Observed criterion F min: 14.7 / Rmerge(I) obs: 0.072 / Rsym value: 0.055 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.5 / Num. unique all: 9708 / Rsym value: 0.188 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MOSFLM6.2.0data reduction
SCALA2.7.5data scaling
TRUNCATE4.1data reduction
SnB0.95phasing
SHARP2.0.0phasing
CNS1.1refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.97 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4397 5 %RANDOM
Rwork0.204 ---
all0.2245 88607 --
obs0.2245 88607 97.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.6171 Å2 / ksol: 0.380688 e/Å3
Displacement parametersBiso max: 77.94 Å2 / Biso mean: 31.42 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.1 Å20 Å2-3.29 Å2
2--7.81 Å20 Å2
3----2.7 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7244 0 0 407 7651
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg23.3
X-RAY DIFFRACTIONx_torsion_impr_deg1.01
X-RAY DIFFRACTIONx_mcbond_it1.161.5
X-RAY DIFFRACTIONx_mcangle_it1.92
X-RAY DIFFRACTIONx_scbond_it1.842
X-RAY DIFFRACTIONx_scangle_it2.742.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.2984694.80.24792390.01411308970885.9
2.4-2.530.2935835.30.236104400.012113981102396.7
2.53-2.690.2835514.90.23107120.012112811126399.8
2.69-2.90.2735765.10.226107450.011113351132199.9
2.9-3.190.25957150.216107810.011113631135299.9
3.19-3.650.2445534.90.207107980.01113591135199.9
3.65-4.590.1925564.90.175107480.008113111130499.9
4.59-29.970.2165384.80.185107470.009112991128599.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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