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- PDB-7p45: Structure of CgGBE in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 7p45
TitleStructure of CgGBE in P212121 space group
Components1,4-alpha-glucan-branching enzyme
KeywordsLYASE / glycogen branching enzyme
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogenin glucosyltransferase activity / fungal biofilm matrix / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm
Similarity search - Function
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 / Glycosyl hydrolase, all-beta / Immunoglobulin E-set ...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 / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
1,4-alpha-glucan-branching enzyme
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBallut, L. / Conchou, L. / Violot, S. / Galisson, F. / Aghajari, N.
CitationJournal: Glycobiology / Year: 2022
Title: The Candida glabrata glycogen branching enzyme structure reveals unique features of branching enzymes of the Saccharomycetaceae phylum.
Authors: Conchou, L. / Martin, J. / Goncalves, I.R. / Galisson, F. / Violot, S. / Guilliere, F. / Aghajari, N. / Ballut, L.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,76511
Polymers81,1441
Non-polymers62110
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint32 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.580, 89.230, 112.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 81143.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: GLC3, CAGL0M03377g / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
References: UniProt: Q6FJV0, 1,4-alpha-glucan branching enzyme
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.5 / Details: 0.1M MES pH 6.5, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.09→47.45 Å / Num. obs: 43538 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rrim(I) all: 0.117 / Net I/σ(I): 14.7
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 6892 / CC1/2: 0.793 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZY

4bzy


Resolution: 2.09→47.45 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 2175 5 %
Rwork0.1905 41331 -
obs0.1926 43506 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 44.9323 Å2 / Biso min: 28.28 Å2
Refinement stepCycle: final / Resolution: 2.09→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5355 0 40 372 5767
Biso mean--52.08 47.16 -
Num. residues----659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.09-2.140.3618450.307386731
2.14-2.190.3335850.269161758
2.19-2.240.34871140.2541216277
2.24-2.30.30151370.241259293
2.3-2.370.31470.23362800100
2.37-2.450.26461480.2222791100
2.45-2.540.28581470.21132799100
2.54-2.640.25031480.22322811100
2.64-2.760.25331470.22582797100
2.76-2.90.25721480.22432807100
2.9-3.090.25381490.21842838100
3.09-3.320.23731480.21542834100
3.32-3.660.23111490.19362827100
3.66-4.190.23931510.16782876100
4.19-5.270.20531530.14662901100
5.28-100.17871590.17023012100
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)
10.7806-0.14850.21860.57480.61080.7195-0.19030.2609-0.0914-0.34290.01260.4885-0.3799-0.3483-0.00060.4333-0.0125-0.06630.5484-0.0090.4853-6.902-6.339-1.095
21.24130.28330.18590.6210.28931.29380.1939-0.0783-0.4064-0.03480.01640.03580.3262-0.15650.00010.3839-0.024-0.04530.38760.08210.43820.685-30.0759.007
31.32850.2950.32211.19340.26640.91860.0507-0.0697-0.15050.1187-0.0251-0.08240.0489-0.0248-00.3115-0.004-0.00220.36450.02880.340715.497-11.42115.017
40.7652-0.2120.5620.92060.00690.7168-0.06020.1093-0.0163-0.1060.0158-0.1519-0.01610.0733-00.3354-0.0386-0.02780.38080.01110.390711.657-7.8951.333
50.46860.16581.04530.8592-0.1410.0898-0.24590.16920.2434-0.19120.17640.1572-0.14840.0751-0.00030.4397-0.0144-0.00280.3971-0.02590.340115.3464.8742.458
60.15450.2597-0.33350.860.02020.5271-0.25420.1471-0.3133-0.37010.244-0.257-0.03170.129200.5753-0.0470.01120.4808-0.0020.437332.57910.956.579
70.27010.38890.230.7390.53850.43330.0650.0259-0.0915-0.02250.0805-0.13890.11960.14720.00020.3811-0.0046-0.0540.4158-0.01930.439939.0558.31419.747
80.24581.42230.17381.29890.30090.6256-0.0228-0.02120.05260.2065-0.0218-0.1939-0.06320.0107-0.00010.43740.005-0.04150.39730.01630.386432.40613.68219.804
91.09270.3634-0.51090.79880.26070.2507-0.0526-0.20640.13940.17150.00740.3543-0.192-0.045900.478-0.0063-0.06960.4003-0.04260.474331.22931.62421.498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:63 )A30 - 63
2X-RAY DIFFRACTION2( CHAIN A AND RESID 64:158 )A64 - 158
3X-RAY DIFFRACTION3( CHAIN A AND RESID 159:320 )A159 - 320
4X-RAY DIFFRACTION4( CHAIN A AND RESID 321:392 )A321 - 392
5X-RAY DIFFRACTION5( CHAIN A AND RESID 393:456 )A393 - 456
6X-RAY DIFFRACTION6( CHAIN A AND RESID 457:496 )A457 - 496
7X-RAY DIFFRACTION7( CHAIN A AND RESID 497:550 )A497 - 550
8X-RAY DIFFRACTION8( CHAIN A AND RESID 551:664 )A551 - 664
9X-RAY DIFFRACTION9( CHAIN A AND RESID 665:706 )A665 - 706

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