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- PDB-1m7x: The X-ray Crystallographic Structure of Branching Enzyme -

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Basic information

Entry
Database: PDB / ID: 1m7x
TitleThe X-ray Crystallographic Structure of Branching Enzyme
Components1,4-alpha-glucan Branching Enzyme
KeywordsTRANSFERASE / alpha/Beta barrel / beta sandwich
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / DNA damage response / cytosol / cytoplasm
Similarity search - Function
Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, SIR / Resolution: 2.3 Å
AuthorsAbad, M.C. / Binderup, K. / Rios-Steiner, J. / Arni, R.K. / Preiss, J. / Geiger, J.H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The X-ray crystallographic structure of Escherichia coli branching enzyme
Authors: Abad, M.C. / Binderup, K. / Rios-Steiner, J. / Arni, R.K. / Preiss, J. / Geiger, J.H.
History
DepositionJul 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-alpha-glucan Branching Enzyme
B: 1,4-alpha-glucan Branching Enzyme
C: 1,4-alpha-glucan Branching Enzyme
D: 1,4-alpha-glucan Branching Enzyme


Theoretical massNumber of molelcules
Total (without water)287,1814
Polymers287,1814
Non-polymers00
Water20,5731142
1
A: 1,4-alpha-glucan Branching Enzyme


Theoretical massNumber of molelcules
Total (without water)71,7951
Polymers71,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-alpha-glucan Branching Enzyme


Theoretical massNumber of molelcules
Total (without water)71,7951
Polymers71,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1,4-alpha-glucan Branching Enzyme


Theoretical massNumber of molelcules
Total (without water)71,7951
Polymers71,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 1,4-alpha-glucan Branching Enzyme


Theoretical massNumber of molelcules
Total (without water)71,7951
Polymers71,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.475, 102.619, 185.060
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
1,4-alpha-glucan Branching Enzyme / Glycogen branching enzyme


Mass: 71795.234 Da / Num. of mol.: 4 / Fragment: Residues 113-728
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P07762, 1,4-alpha-glucan branching enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMsodium HEPES1droppH7.5
25 mg/mlprotein1drop
3100 mMsodium HEPES1reservoirpH7.20

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11161
21161
31161
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97794
SYNCHROTRONAPS 17-ID20.97938
ROTATING ANODERIGAKU RU20031.5418
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDMar 23, 2000
MARRESEARCH2CCDSep 20, 2000
RIGAKU RAXIS IV3IMAGE PLATEJun 20, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CRYSTALSINGLE WAVELENGTHMx-ray1
2CRYSTALSINGLE WAVELENGTHMx-ray1
3osmic focusing opticsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.977941
20.979381
31.54181
ReflectionResolution: 2.3→35 Å / Num. all: 152002 / Num. obs: 151550 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.3 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
dphasesmodel building
SHARPphasing
CNSrefinement
HKL-2000data reduction
DPHASESphasing
RefinementMethod to determine structure: SAD, SIR / Resolution: 2.3→35 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.2653 11792 random
Rwork0.2 --
all-151979 -
obs-136475 -
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19230 0 0 1142 20372
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0075
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.45

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