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- PDB-5e1q: Mutant (D415G) GH97 alpha-galactosidase in complex with Gal-Lac -

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Basic information

Entry
Database: PDB / ID: 5e1q
TitleMutant (D415G) GH97 alpha-galactosidase in complex with Gal-Lac
ComponentsRetaining alpha-galactosidase
KeywordsHYDROLASE / alpha-galactosidase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate binding / metal ion binding
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / : / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 ...Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / : / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Retaining alpha-galactosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.943 Å
AuthorsMatsunaga, K. / Yamashita, K. / Tagami, T. / Yao, M. / Okuyama, M. / Kimura, A.
CitationJournal: FEBS J. / Year: 2017
Title: Efficient synthesis of alpha-galactosyl oligosaccharides using a mutant Bacteroides thetaiotaomicron retaining alpha-galactosidase (BtGH97b).
Authors: Okuyama, M. / Matsunaga, K. / Watanabe, K.I. / Yamashita, K. / Tagami, T. / Kikuchi, A. / Ma, M. / Klahan, P. / Mori, H. / Yao, M. / Kimura, A.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retaining alpha-galactosidase
B: Retaining alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0609
Polymers148,6942
Non-polymers1,3657
Water13,745763
1
A: Retaining alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9844
Polymers74,3471
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retaining alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0765
Polymers74,3471
Non-polymers7294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.620, 100.624, 237.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA21 - 66214 - 655
2ILEILEchain BBB19 - 66212 - 655

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Components

#1: Protein Retaining alpha-galactosidase / BtGH97b / Melibiase


Mass: 74347.094 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-662 / Mutation: D415G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1871 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus RIL (DE3) / References: UniProt: Q8A6L0, alpha-galactosidase
#2: Polysaccharide alpha-D-galactopyranose-(1-1)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-1[DGalpb1-4]DGlcpbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a2122h-1b_1-5][a2112h-1b_1-5]/1-2-3/a1-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG 6000, 0.1 M MES-NaOH (pH 6.2), 3.9 mM beta-lactosyl alpha-d-galactopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→48.1 Å / Num. obs: 106969 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.05 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.089 / Χ2: 0.995 / Net I/σ(I): 18.4 / Num. measured all: 780735
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.94-2.067.30.8570.992.3112006717209164281.07695.5
2.06-2.20.9460.63.8912000616170161690.645100
2.2-2.380.9780.3616.3211188115087150850.388100
2.38-2.60.9880.2439.1710332813961139590.261100
2.6-2.910.9950.14114.739334612655126510.152100
2.91-3.360.9980.0726.888188111255112510.075100
3.36-4.110.9990.03845.3667529953495290.04299.9
4.11-5.790.9990.02858.4552346751675140.03100
5.7910.02164.7430351440943830.02399.4

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Processing

Software
NameVersionClassification
XDSdata processing
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A24

3a24


Resolution: 1.943→42.441 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2139 2 %Random selection
Rwork0.1853 104744 --
obs0.186 106883 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.86 Å2 / Biso mean: 42.7683 Å2 / Biso min: 22.37 Å2
Refinement stepCycle: final / Resolution: 1.943→42.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10229 0 88 763 11080
Biso mean--34.55 41.9 -
Num. residues----1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810602
X-RAY DIFFRACTIONf_angle_d1.07914379
X-RAY DIFFRACTIONf_chiral_restr0.0451533
X-RAY DIFFRACTIONf_plane_restr0.0061852
X-RAY DIFFRACTIONf_dihedral_angle_d12.3433922
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6180X-RAY DIFFRACTION4.438TORSIONAL
12B6180X-RAY DIFFRACTION4.438TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9429-1.98810.37251270.33966154628189
1.9881-2.03780.37251410.303269367077100
2.0378-2.09290.2931430.289470007143100
2.0929-2.15450.34981410.263569257066100
2.1545-2.2240.2911430.238669747117100
2.224-2.30350.26661420.22769417083100
2.3035-2.39570.24721430.207369937136100
2.3957-2.50470.27251430.212869917134100
2.5047-2.63680.28251420.209270127154100
2.6368-2.80190.25891450.201770247169100
2.8019-3.01820.22451430.200970327175100
3.0182-3.32190.19271430.182370347177100
3.3219-3.80230.19991450.164471267271100
3.8023-4.78940.1611460.137571657311100
4.7894-42.45090.18111520.141574377589100
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)
11.3976-0.4593-0.45631.27520.4312.33230.0507-0.19580.07940.3385-0.13630.1947-0.2646-0.27830.08060.566-0.04540.04040.3713-0.03050.2926-67.0258110.862864.5607
21.5083-0.274-0.19690.77780.64482.21370.0163-0.2462-0.18120.4077-0.09190.08390.0622-0.12070.08720.5259-0.05330.01130.32130.02830.287-59.84103.453764.4198
30.9453-0.4097-0.61920.98880.23542.6273-0.0362-0.0404-0.14620.1855-0.1160.08670.2831-0.04280.13370.3491-0.0795-0.01170.19760.01560.2459-56.547996.040944.2139
41.2992-0.9724-0.29471.88110.73352.4445-0.3336-0.2027-0.38730.2880.00590.00290.96710.62810.30530.70730.1730.01780.4380.10490.4038-39.960677.848442.8342
50.5744-0.0448-0.40780.7831-0.07193.1569-0.0108-0.1334-0.01650.0927-0.0930.00690.16030.31350.09630.331-0.0232-0.01460.23970.01860.2798-46.735297.585438.0378
60.3154-0.2283-0.45241.1828-0.00081.4740.2007-0.27140.17080.1937-0.0887-0.2148-1.00880.769-0.06390.654-0.2901-0.02460.5259-0.01910.4101-37.5664117.070236.8822
71.2477-0.19160.19281.34630.12851.4642-0.09450.25660.166-0.41810.0934-0.0101-0.95080.3597-0.00020.9114-0.2095-0.04460.54930.02640.371-39.2341119.220285.2048
80.80410.34080.40490.7403-0.111.9734-0.07940.3091-0.098-0.2398-0.0230.0047-0.38190.15730.07130.5024-0.0121-0.05050.4566-0.03460.3397-48.7784108.740183.8359
92.1689-0.6295-0.48582.00640.25512.3085-0.0520.4416-0.2004-0.34360.0188-0.019-0.38420.48640.02840.4247-0.0854-0.00560.5846-0.0460.3228-40.2216104.744782.1188
101.30890.4495-0.01460.81520.25292.0048-0.09370.11910.0305-0.17120.0306-0.2192-0.76151.0040.04810.4304-0.206-0.04420.52950.00910.3124-34.1823108.7993102.5217
110.61730.0694-0.10920.8224-0.19623.9978-0.04650.1108-0.0996-0.0777-0.0209-0.040.2940.12850.05170.2587-0.0208-0.02110.2602-0.06090.2939-46.421193.7479106.2966
121.36280.28470.29421.2875-0.63832.1580.02350.0643-0.4715-0.1007-0.09240.06031.3217-0.30940.06620.7658-0.13580.00070.3262-0.11090.4812-53.466778.1155110.1887
130.84580.08210.42270.8747-0.14942.341-0.06590.1741-0.0806-0.1138-0.0303-0.0043-0.00530.05460.09970.27040.01530.00790.264-0.03270.2981-47.512797.171107.8512
140.4721-0.1453-0.21261.00690.09442.2365-0.00930.0335-0.00360.0612-0.08120.0868-0.0689-0.32220.08120.2637-0.002-0.01740.2635-0.0370.2991-54.022101.9775123.8667
152.38710.08360.30591.2353-0.23233.2285-0.2520.1320.3968-0.025-0.00520.3159-1.001-0.63180.25440.53150.1633-0.06680.4067-0.04990.4024-58.9566114.978112.6002
161.6775-0.51820.35621.5386-1.03420.8154-0.14860.08760.28330.0176-0.05810.3147-0.7479-0.88670.14810.5690.2955-0.02670.6499-0.08490.5007-65.0046116.6947122.0122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 88 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 142 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 359 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 407 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 562 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 563 through 662 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 22 through 63 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 108 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 142 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 143 through 221 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 222 through 359 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 360 through 407 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 408 through 509 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 510 through 562 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 563 through 607 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 608 through 662 )B0

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