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- PDB-4lq1: Crystal Structure of E.Coli Branching Enzyme in complex with malt... -

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Basic information

Entry
Database: PDB / ID: 4lq1
TitleCrystal Structure of E.Coli Branching Enzyme in complex with maltohexaose
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / Branching enzyme / maltohexaose / linear polysaccharide / starch biosynthetic pathway / alpha/beta barrel
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / 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
alpha-maltose / beta-D-glucopyranose / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsFeng, L. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structures of Escherichia coli Branching Enzyme in Complex with Linear Oligosaccharides.
Authors: Feng, L. / Fawaz, R. / Hovde, S. / Gilbert, L. / Chiou, J. / Geiger, J.H.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: 1,4-alpha-glucan branching enzyme GlgB
B: 1,4-alpha-glucan branching enzyme GlgB
C: 1,4-alpha-glucan branching enzyme GlgB
D: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,37114
Polymers285,1114
Non-polymers2,26010
Water9,962553
1
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4582
Polymers71,2781
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7123
Polymers71,2781
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0544
Polymers71,2781
Non-polymers7773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1465
Polymers71,2781
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.694, 104.113, 186.712
Angle α, β, γ (deg.)90.000, 91.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
1,4-alpha-glucan branching enzyme GlgB / 1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching ...1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching enzyme / Glycogen branching enzyme / BE


Mass: 71277.633 Da / Num. of mol.: 4 / Fragment: UNP residues 117-728
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgB, b3432, JW3395 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07762, 1,4-alpha-glucan branching enzyme
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE TITLE INDICATES THE PRESENCE OF MALTOHEXAOSE, HOWEVER ONLY MONOSACCHARIDE AND ...THE STRUCTURE TITLE INDICATES THE PRESENCE OF MALTOHEXAOSE, HOWEVER ONLY MONOSACCHARIDE AND DISACCHARIDE MOLECULES ARE PRESENT IN THE COORDINATES.

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MAR CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 116155 / Num. obs: 111798 / % possible obs: 96.3 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Χ2: 2.503 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.643.70.439111991.559197.1
2.64-2.753.80.352111811.639196.5
2.75-2.873.80.271111381.773196.8
2.87-3.023.80.201111351.986196
3.02-3.213.80.15111122.289196.1
3.21-3.463.70.106110982.572195.4
3.46-3.813.70.074110072.954195.3
3.81-4.363.50.059110523.418194.8
4.36-5.493.50.051112803.425196.7
5.49-503.80.051115963.562197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å42.7 Å
Translation3 Å42.7 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7445 / SU B: 20.16 / SU ML: 0.206 / SU R Cruickshank DPI: 0.4849 / SU Rfree: 0.2694 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 11224 10 %RANDOM
Rwork0.178 ---
obs0.1826 111712 95.87 %-
all-116546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 161.27 Å2 / Biso mean: 75.6405 Å2 / Biso min: 36.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å2-0.49 Å2
2---3.23 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19417 0 151 553 20121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02120298
X-RAY DIFFRACTIONr_angle_refined_deg1.241.92627588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84252372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38522.9871108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.285153123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.57515169
X-RAY DIFFRACTIONr_chiral_restr0.0910.22779
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116108
X-RAY DIFFRACTIONr_mcbond_it0.83211782
X-RAY DIFFRACTIONr_mcangle_it1.443318894
X-RAY DIFFRACTIONr_scbond_it0.84728516
X-RAY DIFFRACTIONr_scangle_it1.28838694
LS refinement shellResolution: 2.554→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 755 -
Rwork0.241 7183 -
all-7938 -
obs--92.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1986-0.2148-0.07671.5935-1.73165.8567-0.25140.5989-0.5232-0.32980.1540.06990.2663-0.1330.09740.4214-0.13420.06270.3691-0.27460.2381-13.2686-26.826329.9983
21.33230.0341-0.51070.8649-0.191.6791-0.050.1716-0.3234-0.07030.03430.18850.076-0.2230.01570.3473-0.0399-0.02710.12720.01860.1509-24.472-19.656766.8214
32.2561-1.61530.51462.5368-0.72120.8785-0.0919-0.278-0.32970.56920.0911-0.34480.03780.18710.00080.51040.0021-0.23250.12120.06360.300821.1061-25.952489.0671
41.5974-0.37520.03912.0456-0.37460.93270.0485-0.14420.1120.3667-0.0049-0.2519-0.0410.1278-0.04360.4792-0.0318-0.01360.1569-0.01510.04516.71562.909677.3794
51.717-1.4478-0.88093.42121.44291.0781-0.1033-0.0119-0.26740.05830.02250.07130.0545-0.02390.08090.0803-0.02090.07850.2314-0.0140.392446.5136-14.5279-2.4761
60.6922-0.0762-0.20141.21380.44441.2637-0.018-0.14180.0310.11570.0598-0.36310.03990.1557-0.04180.01220.0052-0.04960.2313-0.00260.337543.508912.112325.7028
72.528-0.58380.33254.04-0.95191.4592-0.0662-0.0690.104-0.0129-0.0266-0.103-0.05360.05990.09290.1617-0.01290.01480.25350.03590.1728-0.726445.8868-2.785
80.6306-0.00390.06731.2427-0.54851.1948-0.0111-0.07160.0190.11190.04170.0546-0.0421-0.0818-0.03050.14680.01290.02840.2597-0.02160.20583.535617.649925.3792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 233
2X-RAY DIFFRACTION2A234 - 728
3X-RAY DIFFRACTION3B117 - 389
4X-RAY DIFFRACTION4B390 - 728
5X-RAY DIFFRACTION5C118 - 233
6X-RAY DIFFRACTION6C234 - 728
7X-RAY DIFFRACTION7D117 - 226
8X-RAY DIFFRACTION8D227 - 728

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