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- PDB-1up7: Structure of the 6-phospho-beta glucosidase from Thermotoga marit... -

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Basic information

Entry
Database: PDB / ID: 1up7
TitleStructure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with 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: 2.4 Å
AuthorsVarrot, A. / Yip, V.L. / Withers, S.G. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Nad+ and Metal-Ion Dependent Hydrolysis by Family 4 Glycosidases: Structural Insight Into Specificity for Phospho-Beta-D-Glucosides
Authors: Varrot, A. / Yip, V.L. / Li, Y. / Rajan, S.S. / Yang, X. / Anderson, W.F. / Thompson, J. / Withers, S.G. / Davies, G.J.
History
DepositionSep 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Dec 28, 2016Group: Data collection / Structure summary
Revision 1.4Jul 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_unobs_or_zero_occ_atoms / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 1, 2024Group: 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
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)391,49326
Polymers383,9128
Non-polymers7,58118
Water13,673759
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)195,84314
Polymers191,9564
Non-polymers3,88610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17730 Å2
ΔGint-124.6 kcal/mol
Surface area59410 Å2
MethodPISA
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)195,65012
Polymers191,9564
Non-polymers3,6948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17080 Å2
ΔGint-92.5 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.132, 178.132, 278.927
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
21B
31C
41E
51F
61G
12D
22H

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEUAA1 - 2163 - 218
211METMETLEULEUBB1 - 2163 - 218
311METMETLEULEUCC1 - 2163 - 218
411METMETLEULEUEE1 - 2163 - 218
511METMETLEULEUFF1 - 2163 - 218
611METMETLEULEUGG1 - 2163 - 218
121GLUGLUGLYGLYAA224 - 415226 - 417
221GLUGLUGLYGLYBB224 - 415226 - 417
321GLUGLUGLYGLYCC224 - 415226 - 417
421GLUGLUGLYGLYEE224 - 415226 - 417
521GLUGLUGLYGLYFF224 - 415226 - 417
621GLUGLUGLYGLYGG224 - 415226 - 417
112METMETLEULEUDD1 - 2163 - 218
212METMETLEULEUHH1 - 2163 - 218
122GLUGLUGLYGLYDD224 - 415226 - 417
222GLUGLUGLYGLYHH224 - 415226 - 417

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.99813, 0.05883, -0.01667), (0.04729, 0.91552, 0.39948), (0.03877, 0.39795, -0.91659)248.97224, -43.1702, 175.04907
2given(-0.90581, 0.08992, -0.41403), (0.09531, -0.90892, -0.40593), (-0.41282, -0.40715, 0.81474)276.46356, 103.04469, 86.18145
3given(0.89892, -0.13028, 0.41829), (-0.14877, -0.9888, 0.01174), (0.41207, -0.07279, -0.90824)-25.26489, 94.02693, 145.7513
4given(0.99179, 0.01752, 0.12665), (-0.01998, 0.99963, 0.01823), (-0.12628, -0.02062, 0.99178)-102.1575, 0.94903, 17.53061
5given(-0.98654, 0.11517, -0.11612), (0.0616, 0.91939, 0.38849), (0.1515, 0.37611, -0.91411)166.05394, -43.79459, 161.50446
6given(-0.93768, 0.02955, -0.34624), (0.10371, -0.92717, -0.36), (-0.33166, -0.37347, 0.86632)186.60518, 97.98878, 69.9372
7given(0.9391, -0.14985, 0.30923), (-0.14212, -0.98871, -0.04751), (0.31286, 0.00067, -0.9498)-107.7821, 99.29242, 159.54529

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Components

#1: Protein
6-PHOSPHO-BETA-GLUCOSIDASE


Mass: 47989.051 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
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHIS 0, PART OF THE INSERTED N TERMINAL HIS TAG ARG -1, 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 %
Description: THE STARTING MODEL USED WAS THE SELENOMET STRUCTURE SOLVED IN THE SAME SPACE GROUP
Crystal growpH: 4.6
Details: 200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 25% PEG500DME, 0.2MM NAD+, 1MM PNP-BETA-D-GLUCOSE-6-PHOSPHATE, 2MM MNS04. PROTEIN AT 5 MG/ML WITH THE COFACTORS IN THE SAME CONCENTRATION AS ABOVE.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 170857 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SE-MET STRUCTURE

Resolution: 2.4→19.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.116 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND ATOM HAVE BEEN GIVEN AN OCCUPANCY OF 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 8549 5 %RANDOM
Rwork0.199 ---
obs0.201 162307 98.3 %-
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: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26560 0 490 759 27809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02227608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.99237287
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86853257
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_restr0.1040.24164
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220411
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.213025
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4391.516254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.957226334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89311354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1354.510953
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1617tight positional0.070.05
12B1617tight positional0.070.05
13C1617tight positional0.050.05
14E1617tight positional0.040.05
15F1617tight positional0.040.05
16G1617tight positional0.050.05
21D1628tight positional0.080.05
11A1662medium positional0.450.5
12B1662medium positional0.460.5
13C1662medium positional0.440.5
14E1662medium positional0.40.5
15F1662medium positional0.450.5
16G1662medium positional0.460.5
21D1672medium positional0.350.5
11A1617tight thermal0.150.5
12B1617tight thermal0.10.5
13C1617tight thermal0.110.5
14E1617tight thermal0.090.5
15F1617tight thermal0.090.5
16G1617tight thermal0.10.5
21D1628tight thermal0.140.5
11A1662medium thermal1.052
12B1662medium thermal0.772
13C1662medium thermal0.842
14E1662medium thermal0.722
15F1662medium thermal0.72
16G1662medium thermal0.722
21D1672medium thermal0.722
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 497
Rwork0.22 9862
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)
11.5026-0.3748-0.44721.1279-0.12190.73420.0165-0.0546-0.00750.1076-0.0258-0.1774-0.03990.20630.00930.1677-0.0144-0.06110.087-0.05250.0644146.15658.725100.031
21.37890.90350.34381.65470.63151.8790.0533-0.16670.2080.0834-0.170.5144-0.127-0.55170.11660.1610.04380.02720.217-0.06910.2384104.91157.194112.74
31.1967-0.81060.26251.2241-0.14721.83060.03920.0611-0.0979-0.0306-0.03620.25750.2058-0.3398-0.0030.153-0.0628-0.02780.1063-0.00310.1073107.96923.21683.269
41.1140.61640.5762.5231-0.03841.07920.0816-0.1268-0.13820.4001-0.0049-0.46980.07940.1223-0.07670.27350.0177-0.08160.0791-0.00360.1425140.07515.462111.161
51.6580.0145-0.02184.2605-0.08521.0085-0.03450.07360.0262-0.38590.0703-1.3965-0.11290.3468-0.03580.3226-0.09060.07510.2108-0.09190.714855.83158.47796.921
62.38911.09030.38991.83240.33161.5830.0571-0.50910.37650.3776-0.08510.273-0.255-0.34370.0280.35130.0640.00070.2836-0.08040.23417.21457.842114.369
71.4338-0.79480.42241.6837-0.06072.12110.07910.1247-0.2354-0.0002-0.04660.19120.2879-0.3419-0.03250.2156-0.0659-0.00250.15710.00780.179116.83922.93686.111
81.78180.13070.60352.4506-0.24421.14830.0621-0.1988-0.07550.424-0.0202-0.70670.11310.2363-0.04190.38620.0522-0.17080.18470.01780.490151.27115.847110.698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 415
2X-RAY DIFFRACTION2B1 - 415
3X-RAY DIFFRACTION3C1 - 415
4X-RAY DIFFRACTION4D1 - 415
5X-RAY DIFFRACTION5E1 - 415
6X-RAY DIFFRACTION6F1 - 415
7X-RAY DIFFRACTION7G1 - 415
8X-RAY DIFFRACTION8H1 - 415

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