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- PDB-1up6: Structure of the 6-phospho-beta glucosidase from Thermotoga marit... -

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Basic information

Entry
Database: PDB / ID: 1up6
TitleStructure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate
Components6-PHOSPHO-BETA-GLUCOSIDASE
KeywordsHYDROLASE / 6-PHOSPHO-BETA-GLUCOSIDASE / FAMILY4 HYDROLASE / NAD DEPENDENT
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 6-phospho-beta-glucosidase BglT
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVarrot, A. / Yip, V.L. / Withers, S.G. / Davies, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 Beta-Glycosidase from Thermotoga Maritima.
Authors: Yip, V.L. / Varrot, A. / Davies, G.J. / Rajan, S.S. / Yang, X. / Thompson, J. / Anderson, W.F. / Withers, S.G.
History
DepositionSep 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHO-BETA-GLUCOSIDASE
B: 6-PHOSPHO-BETA-GLUCOSIDASE
C: 6-PHOSPHO-BETA-GLUCOSIDASE
D: 6-PHOSPHO-BETA-GLUCOSIDASE
E: 6-PHOSPHO-BETA-GLUCOSIDASE
F: 6-PHOSPHO-BETA-GLUCOSIDASE
G: 6-PHOSPHO-BETA-GLUCOSIDASE
H: 6-PHOSPHO-BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,45022
Polymers385,2818
Non-polymers3,16914
Water10,233568
1
A: 6-PHOSPHO-BETA-GLUCOSIDASE
B: 6-PHOSPHO-BETA-GLUCOSIDASE
C: 6-PHOSPHO-BETA-GLUCOSIDASE
D: 6-PHOSPHO-BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,89914
Polymers192,6404
Non-polymers2,25910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: 6-PHOSPHO-BETA-GLUCOSIDASE
F: 6-PHOSPHO-BETA-GLUCOSIDASE
G: 6-PHOSPHO-BETA-GLUCOSIDASE
H: 6-PHOSPHO-BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5518
Polymers192,6404
Non-polymers9104
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)179.438, 179.438, 282.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 1 - 415 / Label seq-ID: 2 - 416

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD
13EE
23GG
14FF
24HH

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.99794, 0.05086, 0.03913), (0.06261, 0.90547, 0.41977), (-0.01409, 0.42136, -0.90679)245.18015, -47.48618, 181.27386
2given(-0.91131, 0.09364, -0.40093), (0.08785, -0.90714, -0.41155), (-0.40224, -0.41028, 0.81846)277.63678, 106.20757, 85.19185
3given(0.90405, -0.15226, 0.39938), (-0.14223, -0.98831, -0.05482), (0.40306, -0.00725, -0.91515)-22.79163, 101.49026, 146.73297
4given(0.99061, -0.01389, -0.13598), (0.01125, 0.99973, -0.02014), (0.13622, 0.01842, 0.99051)105.221, 1.50793, -4.83549
5given(-0.98832, 0.05836, 0.1408), (0.1108, 0.90947, 0.40074), (-0.10467, 0.41165, -0.90531)144.13344, -41.77715, 183.41354
6given(-0.9414, 0.09446, -0.32378), (0.03814, -0.92401, -0.38045), (-0.33512, -0.37051, 0.86627)188.9623, 113.32472, 39.78714
7given(0.94232, -0.14195, 0.30313), (-0.15286, -0.98817, 0.01244), (0.29778, -0.05806, -0.95287)66.61498, 82.10957, 192.60754

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDEFGH

#1: Protein
6-PHOSPHO-BETA-GLUCOSIDASE


Mass: 48160.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: SYNTHETIC GENE / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9X108, endo-1,3(4)-beta-glucanase
#4: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 580 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsHIS 0, PART OF THE INSERTED N-TERMINAL HIS TAG

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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: 2.8 Å3/Da / Density % sol: 56.3 %
Crystal growpH: 4.6
Details: 200 MM SODIUM FORMATE, 100MM SODIUM ACETATE PH 4.6, 5% PEG 4000. PROTEIN AT 5 MG/ML

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorDate: Dec 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 149303 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UP4

1up4


Resolution: 2.55→19.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.719 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND ATOM HAVE BEEN GIBEN AN OCCUPANCY OF 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 7464 5 %RANDOM
Rwork0.2 ---
obs0.202 141836 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.76 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26155 0 189 568 26912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02226863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.97836230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90553195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.24043
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.211552
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.21015
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4441.515995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.951225918
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.078310868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1714.510312
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1624tight positional0.050.05
2B1612tight positional0.050.05
3E1548tight positional0.040.05
4F1580tight positional0.040.05
1A1664medium positional0.40.5
2B1660medium positional0.410.5
3E1592medium positional0.460.5
4F1629medium positional0.440.5
1A1624tight thermal0.130.5
2B1612tight thermal0.120.5
3E1548tight thermal0.130.5
4F1580tight thermal0.080.5
1A1664medium thermal0.772
2B1660medium thermal0.82
3E1592medium thermal0.732
4F1629medium thermal0.532
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 549
Rwork0.208 10236

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