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- PDB-5wu7: Crystal structure of GH57-type branching enzyme from hyperthermop... -

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Basic information

Entry
Database: PDB / ID: 5wu7
TitleCrystal structure of GH57-type branching enzyme from hyperthermophilic archaeon Pyrococcus horikoshii
ComponentsUncharacterized protein
KeywordsHYDROLASE / enzyme / amylase / glycogen branching enzyme
Function / homology
Function and homology information


alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme activity
Similarity search - Function
: / 1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain ...: / 1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNa, S. / Jo, I. / Ha, N.-C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii.
Authors: Na, S. / Park, M. / Jo, I. / Cha, J. / Ha, N.C.
History
DepositionDec 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0614
Polymers133,8772
Non-polymers1842
Water1,72996
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0312
Polymers66,9391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0312
Polymers66,9391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.857, 42.326, 122.227
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein / 1 / 4-alpha-glucan-branching protein


Mass: 66938.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GOL
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O50094
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.3
Details: 20 mM citric acid, 10% (w/v) PEG 3350, 80 mM Bis-Tris propane pH 9.3, 2 mM tris (2-carboxyethyl) phosphine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→33.521 Å / Num. obs: 44048 / % possible obs: 95 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.08 / % possible all: 72.1

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8T

3n8t


Resolution: 2.31→33.521 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.2597 2249 5.11 %
Rwork0.1998 --
obs0.2028 44048 79.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→33.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8901 0 12 96 9009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039182
X-RAY DIFFRACTIONf_angle_d0.55412401
X-RAY DIFFRACTIONf_dihedral_angle_d4.4325375
X-RAY DIFFRACTIONf_chiral_restr0.0411246
X-RAY DIFFRACTIONf_plane_restr0.0051574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3098-2.36010.37640.24631269X-RAY DIFFRACTION39
2.3601-2.41490.3432840.2481572X-RAY DIFFRACTION49
2.4149-2.47530.3424820.23611720X-RAY DIFFRACTION52
2.4753-2.54220.3172950.23451884X-RAY DIFFRACTION58
2.5422-2.6170.31971130.24332042X-RAY DIFFRACTION63
2.617-2.70140.31851250.24562212X-RAY DIFFRACTION68
2.7014-2.79790.30631610.24472399X-RAY DIFFRACTION74
2.7979-2.90990.31841370.23542665X-RAY DIFFRACTION82
2.9099-3.04230.28981680.22792939X-RAY DIFFRACTION90
3.0423-3.20250.28771960.22023223X-RAY DIFFRACTION99
3.2025-3.4030.26791920.22223207X-RAY DIFFRACTION100
3.403-3.66550.25581230.20133324X-RAY DIFFRACTION100
3.6655-4.03380.25882120.18173254X-RAY DIFFRACTION100
4.0338-4.61620.20871690.16793328X-RAY DIFFRACTION100
4.6162-5.8110.23181570.16943324X-RAY DIFFRACTION99
5.811-33.52410.19651710.17273437X-RAY DIFFRACTION99

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