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- PDB-1u8x: CRYSTAL STRUCTURE OF GLVA FROM BACILLUS SUBTILIS, A METAL-REQUIRI... -

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Basic information

Entry
Database: PDB / ID: 1u8x
TitleCRYSTAL STRUCTURE OF GLVA FROM BACILLUS SUBTILIS, A METAL-REQUIRING, NAD-DEPENDENT 6-PHOSPHO-ALPHA-GLUCOSIDASE
ComponentsMaltose-6'-phosphate glucosidase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI / protein structure initiative / MCSG / GLUCOSIDASE / NAD-DEPENDENT / Midwest Center for Structural Genomics
Function / homology
Function and homology information


maltose-6'-phosphate glucosidase / maltose-6'-phosphate glucosidase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carbohydrate metabolic process / metal ion binding
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 / Maltose-6'-phosphate glucosidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsRajan, S.S. / Yang, X. / Collart, F. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: STRUCTURE / Year: 2004
Title: Novel Catalytic Mechanism of Glycoside Hydrolysis Based on the Structure of an NAD(+)/Mn(2+)-Dependent Phospho-alpha-Glucosidase from Bacillus subtilis.
Authors: Rajan, S.S. / Yang, X. / Collart, F. / Yip, V.L. / Withers, S.G. / Varrot, A. / Thompson, J. / Davies, G.J. / Anderson, W.F.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionAug 24, 2004ID: 1NRH
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 1.4Apr 3, 2024Group: 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
X: Maltose-6'-phosphate glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0634
Polymers54,0841
Non-polymers9783
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.604, 102.017, 144.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Maltose-6'-phosphate glucosidase / 6-phospho-alpha-D-glucosidase / 6-phosphoryl-O-alpha-D-glucopyranosyl:phosphoglucohydrolase


Mass: 54084.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: glvA, glvG, glv-1 / Plasmid: PMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P54716, maltose-6'-phosphate glucosidase
#2: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.8 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M MgCl2, 0.1M Tris-Cl, pH8.0, 28% PEG4000, 10% (v/v)glycerol, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77.4 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 275160 / Num. obs: 38535 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.569 / Num. unique all: 2536 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SAD
Starting model: AUTO-BUILT MODEL FROM RESOLVE

Resolution: 2.05→30.02 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.017 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3655 10 %RANDOM
Rwork0.195 ---
all0.197 33021 --
obs0.197 33021 95 %-
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: 28.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--3.16 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 61 162 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223587
X-RAY DIFFRACTIONr_bond_other_d0.0020.023178
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9794871
X-RAY DIFFRACTIONr_angle_other_deg0.83237419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345434
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_restr0.0830.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023940
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined0.2150.2823
X-RAY DIFFRACTIONr_nbd_other0.2390.23938
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.22068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4210.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7431.52175
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40623517
X-RAY DIFFRACTIONr_scbond_it2.19431412
X-RAY DIFFRACTIONr_scangle_it3.5764.51354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 252
Rwork0.245 2156
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)
10.67930.0208-0.14810.5291-0.24570.7966-0.1187-0.2596-0.35380.0560.0194-0.09180.19840.03930.09930.18030.0390.03480.10570.1420.192617.802780.742623.1372
21.48860.0871-0.10630.640.02220.7724-0.0449-0.3611-0.05230.12150.0183-0.0406-0.02970.1060.02660.14220.0507-0.01870.1625-0.01690.074416.6015103.282522.1859
31.23870.5618-1.25383.4522-4.92835.7911-0.0098-0.355-0.24850.3633-0.2923-0.3858-0.290.35370.30210.2768-0.028-0.05840.25520.05330.219133.978685.338328.6581
40.9265-0.0993-0.0730.3973-0.17190.5651-0.08510.0292-0.1168-0.07780.0248-0.07130.09450.03310.06030.1680.00980.040.0656-0.01610.13821.303390.48852.0985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA3 - 16926 - 192
2X-RAY DIFFRACTION2XA170 - 271193 - 294
3X-RAY DIFFRACTION2XA320 - 367343 - 390
4X-RAY DIFFRACTION3XA272 - 319295 - 342
5X-RAY DIFFRACTION4XA368 - 444391 - 467

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