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Basic information

Entry
Database: PDB / ID: 2gft
TitleCrystal structure of the E263A nucleophile mutant of Bacillus licheniformis endo-beta-1,4-galactanase in complex with galactotriose
ComponentsGlycosyl Hydrolase Family 53
KeywordsHYDROLASE / beta-alpha-8-barrel / protein-oligosaccharide complex / nucleophile inactive mutant
Function / homology
Function and homology information


arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 53 / Glycosyl hydrolase family 53 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4beta-beta-galactotriose / : / Endo-beta-1,4-galactanase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsWelner, D. / Le Nours, J. / De Maria, L. / Jorgensen, C.T. / Christensen, L.L.H. / Larsen, S. / Lo Leggio, L.
Citation
Journal: To be Published
Title: Oligosaccharide binding of Bacillus licheniformis endo-beta-1,4-galactanase
Authors: Le Nours, J. / De Maria, L. / Welner, D. / Jorgensen, C.T. / Christensen, L.L.H. / Larsen, S. / Lo Leggio, L.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The Structure of Endo-beta-1,4-galactanase from Bacillus licheniformis in Complex with Two Oligosaccharide Products
Authors: Ryttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L.H. / Bjornvad, M. / Larsen, S.
History
DepositionMar 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_source
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / 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_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl Hydrolase Family 53
B: Glycosyl Hydrolase Family 53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5306
Polymers87,4412
Non-polymers1,0894
Water5,296294
1
A: Glycosyl Hydrolase Family 53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2653
Polymers43,7201
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl Hydrolase Family 53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2653
Polymers43,7201
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.273, 79.354, 103.906
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B
451A
461B
471A
481B
491A
501B
511A
521B
531A
541B
551A
561B
571A
581B
591A
601B
611A
621B
631A
641B
651A
661B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEU5AA11 - 1211 - 12
21GLYGLYLEULEU5BB11 - 1211 - 12
32TYRTYRTYRTYR3AA1313
42TYRTYRTYRTYR3BB1313
53VALVALLEULEU1AA14 - 2014 - 20
63VALVALLEULEU1BB14 - 2014 - 20
74ARGARGLYSLYS3AA21 - 2221 - 22
84ARGARGLYSLYS3BB21 - 2221 - 22
95ASPASPLEULEU1AA23 - 8823 - 88
105ASPASPLEULEU1BB23 - 8823 - 88
116GLUGLUGLUGLU3AA8989
126GLUGLUGLUGLU3BB8989
137LYSLYSPHEPHE1AA90 - 13290 - 132
147LYSLYSPHEPHE1BB90 - 13290 - 132
158GLUGLUGLUGLU3AA133133
168GLUGLUGLUGLU3BB133133
179ASPASPLYSLYS1AA134 - 144134 - 144
189ASPASPLYSLYS1BB134 - 144134 - 144
1910GLNGLNGLNGLN3AA145145
2010GLNGLNGLNGLN3BB145145
2111SERSERSERSER1AA146 - 187146 - 187
2211SERSERSERSER1BB146 - 187146 - 187
2312GLNGLNGLNGLN3AA188188
2412GLNGLNGLNGLN3BB188188
2513ALAALAVALVAL1AA189 - 190189 - 190
2613ALAALAVALVAL1BB189 - 190189 - 190
2714ARGARGARGARG3AA191191
2814ARGARGARGARG3BB191191
2915GLUGLUGLUGLU5AA192192
3015GLUGLUGLUGLU5BB192192
3116THRTHRLEULEU1AA193 - 219193 - 219
3216THRTHRLEULEU1BB193 - 219193 - 219
3317HISHISARGARG3AA220 - 221220 - 221
3417HISHISARGARG3BB220 - 221220 - 221
3518HISHISHISHIS1AA222222
3618HISHISHISHIS1BB222222
3719HISHISHISHIS3AA223223
3819HISHISHISHIS3BB223223
3920VALVALGLYGLY1AA224 - 311224 - 311
4020VALVALGLYGLY1BB224 - 311224 - 311
4121GLUGLUGLUGLU3AA312312
4221GLUGLUGLUGLU3BB312312
4322ALAALAHISHIS3AA313 - 331313 - 331
4422ALAALAHISHIS3BB313 - 331313 - 331
4523ARGARGARGARG3AA332332
4623ARGARGARGARG3BB332332
4724LEULEUPROPRO1AA333 - 357333 - 357
4824LEULEUPROPRO1BB333 - 357333 - 357
4925GLUGLUGLUGLU3AA358358
5025GLUGLUGLUGLU3BB358358
5126ASPASPLYSLYS1AA359 - 362359 - 362
5226ASPASPLYSLYS1BB359 - 362359 - 362
5327TRPTRPTRPTRP5AA363363
5427TRPTRPTRPTRP5BB363363
5528PHEPHEPHEPHE1AA364 - 377364 - 377
5628PHEPHEPHEPHE1BB364 - 377364 - 377
5729LYSLYSLYSLYS3AA378378
5829LYSLYSLYSLYS3BB378378
5930GLYGLYPHEPHE1AA379 - 388379 - 388
6030GLYGLYPHEPHE1BB379 - 388379 - 388
6131GLNGLNGLNGLN3AA389389
6231GLNGLNGLNGLN3BB389389
6332TYRTYRTHRTHR1AA390 - 395390 - 395
6432TYRTYRTHRTHR1BB390 - 395390 - 395
6533PROPROPROPRO5AA396396
6633PROPROPROPRO5BB396396

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Components

#1: Protein Glycosyl Hydrolase Family 53


Mass: 43720.398 Da / Num. of mol.: 2 / Mutation: E263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Bacillus subtilis (bacteria)
References: GenBank: 52005769, UniProt: Q65CX5*PLUS, arabinogalactan endo-beta-1,4-galactanase
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose / 4beta-beta-galactotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-galactotriose
DescriptorTypeProgram
DGalpb1-4DGalpb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-Galp]{[(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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 24-35% (w/v) PEG 1500 Soak: few seconds, 0.3-0.5 M methyl- (1 4)-galactotetraoside, 15% PEG 1500 and 15% PEG 400., VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 31812 / % possible obs: 88 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.346 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.186 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23156 1606 5.1 %RANDOM
Rwork0.17985 ---
obs0.18253 30191 87.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.164 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å21.56 Å2
2--2.71 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5997 0 70 294 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9378478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68524.846293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94715945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9741520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2907
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024817
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23022
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24252
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2439
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.53898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02226080
X-RAY DIFFRACTIONr_scbond_it1.53332731
X-RAY DIFFRACTIONr_scangle_it2.4494.52398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2786tight positional0.080.05
21medium positional0.790.5
187loose positional1.185
2786tight thermal0.130.5
21medium thermal0.392
187loose thermal2.5810
LS refinement shellResolution: 2.3→2.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 91 -
Rwork0.235 1884 -
obs--75.1 %

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