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- PDB-5d0f: Crystal Structure of the Candida Glabrata Glycogen Debranching En... -

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Basic information

Entry
Database: PDB / ID: 5d0f
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (E564Q) in complex with maltopentaose
ComponentsUncharacterized protein
KeywordsSUGAR BINDING PROTEIN / TIM barrel / (alpha/alpha)6 barrel / hydrolase
Function / homology
Function and homology information


amylo-alpha-1,6-glucosidase / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / glycogen catabolic process / glycogen biosynthetic process / cytoplasm
Similarity search - Function
Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, glucanotransferase domain / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Glycogen debranching enzyme, C-terminal / Amylo-alpha-1,6-glucosidase ...Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, glucanotransferase domain / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Glycogen debranching enzyme, C-terminal / Amylo-alpha-1,6-glucosidase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltotriose / alpha-maltotetraose / alpha-maltopentaose / Glycogen debranching enzyme
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsZhai, L. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology2011CB910500 China
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.
Authors: Zhai, L. / Feng, L. / Xia, L. / Yin, H. / Xiang, S.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,60113
Polymers348,9452
Non-polymers7,65711
Water00
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6347
Polymers174,4721
Non-polymers4,1626
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9676
Polymers174,4721
Non-polymers3,4955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.070, 202.010, 135.240
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 174472.422 Da / Num. of mol.: 2 / Mutation: E564Q
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: CAGL0G09977g / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q6FSK0
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG 5000 MME, 0.1 M Hepes, 5% tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→132.609 Å / Num. all: 59857 / Num. obs: 59857 / % possible obs: 96.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 86.19 Å2 / Rpim(I) all: 0.059 / Rrim(I) all: 0.108 / Rsym value: 0.09 / Net I/av σ(I): 6.659 / Net I/σ(I): 8.5 / Num. measured all: 187312
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.3-3.482.90.4881.62462586120.3350.5960.4882.194.8
3.48-3.692.90.3022.52451383150.2050.3670.3023.397.2
3.69-3.943.10.2113.62427879270.140.2540.2114.897.9
3.94-4.263.20.1415.32350573160.0910.1680.1417.197.1
4.26-4.673.30.0987.22181667070.0620.1160.0989.797
4.67-5.223.20.0838.11957960310.0520.0980.08311.496.5
5.22-6.023.10.0788.51663453030.0490.0920.07811.795.7
6.02-7.383.20.05311.81375942740.0340.0630.05314.391.4
7.38-10.443.50.025241216234870.0150.0290.02520.495.7
10.44-49.0533.40.02911.6644118850.020.0360.02923.193.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALA3.3.21data scaling
MOLREP11.2.08phasing
PDB_EXTRACT3.15data extraction
MOSFLM7.2.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D06

5d06


Resolution: 3.3→49.053 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 3069 5.13 %RANDOM
Rwork0.1922 ---
obs0.1941 59814 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24556 0 514 0 25070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01625727
X-RAY DIFFRACTIONf_angle_d2.02134953
X-RAY DIFFRACTIONf_dihedral_angle_d19.7469728
X-RAY DIFFRACTIONf_chiral_restr0.1063873
X-RAY DIFFRACTIONf_plane_restr0.014436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.35160.37111370.31722502X-RAY DIFFRACTION94
3.3516-3.40650.30781190.31272555X-RAY DIFFRACTION95
3.4065-3.46520.32671310.28752580X-RAY DIFFRACTION95
3.4652-3.52820.30671420.28622580X-RAY DIFFRACTION97
3.5282-3.59610.3291170.26612618X-RAY DIFFRACTION97
3.5961-3.66940.31961490.25592614X-RAY DIFFRACTION97
3.6694-3.74920.28351310.24172609X-RAY DIFFRACTION97
3.7492-3.83640.28881270.2312613X-RAY DIFFRACTION98
3.8364-3.93230.24581540.21492614X-RAY DIFFRACTION98
3.9323-4.03860.25251430.20492637X-RAY DIFFRACTION97
4.0386-4.15730.22141380.19162605X-RAY DIFFRACTION97
4.1573-4.29150.20721520.18012606X-RAY DIFFRACTION97
4.2915-4.44470.21291400.17122600X-RAY DIFFRACTION97
4.4447-4.62260.19471540.16342577X-RAY DIFFRACTION97
4.6226-4.83280.19021310.16242623X-RAY DIFFRACTION96
4.8328-5.08730.22761410.16392568X-RAY DIFFRACTION96
5.0873-5.40570.21061300.16722597X-RAY DIFFRACTION96
5.4057-5.82250.21711650.18622568X-RAY DIFFRACTION95
5.8225-6.40720.24671460.18132476X-RAY DIFFRACTION92
6.4072-7.33170.2081410.17062436X-RAY DIFFRACTION91
7.3317-9.22720.16971490.14832610X-RAY DIFFRACTION96
9.2272-49.05870.17891320.15962557X-RAY DIFFRACTION93
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)
11.85850.08730.32623.94480.42372.20140.1227-0.0987-0.01860.10660.03610.42890.2129-0.4133-0.07470.3017-0.1489-0.0161.18460.0810.560125.3102-12.338949.7385
22.4473-0.4456-0.67223.7835-0.12512.41740.21870.01850.36850.01980.0965-0.4974-0.21810.3368-0.23680.23360.05370.02980.9564-0.13910.8357-16.0887-4.504837.4162
30.9424-0.20920.29281.12720.2341.07270.19450.0336-0.28790.05940.017-0.08560.43810.2758-0.21780.45980.0762-0.14221.20550.03060.748148.5051-26.95543.2416
40.8561-0.3403-0.34271.06490.2321.30770.2240.00580.3618-0.11920.0161-0.0951-0.5486-0.3259-0.23490.54020.27510.18991.0473-0.02120.8612-39.728710.783235.7238
50.5682-0.59691.34042.0424-1.13993.32150.11270.2924-0.0035-0.0350.0103-0.28720.35570.3257-0.13640.6563-0.0652-0.10671.3517-0.05650.792732.1848-32.48193.629
60.74720.1082-0.90240.70491.13373.4191-0.07650.4357-0.0997-0.1226-0.04650.4674-0.4445-0.59430.02731.03770.31970.20551.44470.10331.0605-31.858915.4727-6.5177
72.27430.9830.94721.08440.14471.26070.05230.14540.0315-0.1609-0.0623-0.1770.26690.5254-0.0163-0.18530.2188-0.17031.7831-0.0550.664671.2446-12.350245.2424
81.89030.6341-1.07461.2641-0.08611.70610.103-0.0120.0424-0.1326-0.1704-0.049-0.1209-0.6330.10670.06380.35310.08541.58790.00920.7536-61.9593-3.100442.6296
91.2749-0.12690.26733.18410.4151.917-0.0565-0.13470.29890.3960.153-0.5617-0.3260.3326-0.02770.1879-0.1189-0.09211.2857-0.05680.668945.092215.264159.5814
102.2239-0.4763-0.41643.6128-0.06652.3869-0.2034-0.3473-0.37860.52260.24370.72480.2719-0.375-0.06180.32830.11380.11951.00950.16610.8026-34.3291-31.281751.4234
112.11740.37440.46843.71120.41252.007-0.1333-0.13310.8435-0.23530.01971.2993-0.5442-0.57520.13760.44920.2099-0.05331.09620.04941.34112.409732.115552.4465
122.00450.0444-0.46663.0695-0.35182.4916-0.2775-0.095-0.797-0.0160.1829-0.19760.73560.4950.10670.55250.314-0.0190.895-0.09441.0237-4.7216-49.333537.2582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:131))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 3:131))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 132:237) or (resseq 499:749))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 132:237) or (resseq 499:749))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 238:498))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 238:498))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 750:869))
8X-RAY DIFFRACTION8chain 'B' and ((resseq 750:869))
9X-RAY DIFFRACTION9chain 'A' and ((resseq 870:1022))
10X-RAY DIFFRACTION10chain 'B' and ((resseq 870:1022))
11X-RAY DIFFRACTION11chain 'A' and ((resseq 1023:1528))
12X-RAY DIFFRACTION12chain 'B' and ((resseq 1023:1528))

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