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- PDB-6dux: 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glu... -

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Basic information

Entry
Database: PDB / ID: 6dux
Title2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD.
Components6-phospho-alpha-glucosidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phospho-alpha-glucosidase / NAD
Function / homology
Function and homology information


maltose-6'-phosphate glucosidase / maltose-6'-phosphate glucosidase activity / sucrose metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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
ACETATE ION / BICARBONATE ION / (2S)-2-hydroxybutanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 6-phospho-alpha-glucosidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJun 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phospho-alpha-glucosidase
B: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,61214
Polymers100,6692
Non-polymers1,94212
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-58 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.226, 85.226, 228.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

21B-725-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 6-phospho-alpha-glucosidase


Mass: 50334.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: aglB / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic
References: UniProt: Q9AGA6, maltose-6'-phosphate glucosidase

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Non-polymers , 7 types, 370 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 10.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM NAD; Screen: Classics II (B11) 2.1M DL-malic acid pH 7.0; Cryo: Screen + 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 46596 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Rsym value: 0.102 / Χ2: 1.367 / Net I/σ(I): 22.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 3 / Num. unique obs: 2254 / CC1/2: 0.854 / Rpim(I) all: 0.282 / Rrim(I) all: 0.832 / Rsym value: 0.782 / Χ2: 1.009 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.89 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.611 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19129 2358 5.1 %RANDOM
Rwork0.15427 ---
obs0.15612 44168 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----3.05 Å2
Refinement stepCycle: 1 / Resolution: 2.25→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 122 359 7288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0147149
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176382
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.7029725
X-RAY DIFFRACTIONr_angle_other_deg0.4441.70214964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2725877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1422.67367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2591542
X-RAY DIFFRACTIONr_chiral_restr0.0680.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.028029
X-RAY DIFFRACTIONr_gen_planes_other0.0370.021309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7093.2733491
X-RAY DIFFRACTIONr_mcbond_other1.7053.2733490
X-RAY DIFFRACTIONr_mcangle_it2.654.8984367
X-RAY DIFFRACTIONr_mcangle_other2.6494.8994368
X-RAY DIFFRACTIONr_scbond_it2.343.6563657
X-RAY DIFFRACTIONr_scbond_other2.3393.6563657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5995.375357
X-RAY DIFFRACTIONr_long_range_B_refined5.73740.0418200
X-RAY DIFFRACTIONr_long_range_B_other5.62839.8228135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.252→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 154 -
Rwork0.214 3209 -
obs--99.12 %
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)
12.34820.8918-0.53132.53770.7412.6091-0.0704-0.34370.09880.2619-0.114-0.0408-0.11160.08490.18440.1398-0.0711-0.08180.2226-0.02590.104624.05720.156441.0108
20.79380.1283-0.1180.7303-0.25581.28570.0345-0.07350.01840.2225-0.1115-0.0913-0.26690.17310.0770.1168-0.0801-0.01130.0895-0.05990.143517.738825.533721.014
30.8217-0.30670.630.2424-0.41131.3843-0.0754-0.10210.26780.2067-0.0603-0.0904-0.58620.0720.13570.3912-0.1173-0.03710.1098-0.10320.272617.660239.453724.0426
40.77140.2329-0.13370.5919-0.14981.61950.026-0.06820.07390.0481-0.0734-0.1131-0.1540.20060.04740.0262-0.0357-0.00380.0598-0.02580.122819.101521.924611.7228
51.53870.1621-0.40350.8070.32991.8352-0.0434-0.0480.2683-0.105-0.06050.4113-0.1901-0.46650.10390.03610.0342-0.03850.257-0.04880.2915-28.306710.666212.7099
60.6154-0.2229-0.67710.7610.01063.2597-0.0567-0.1358-0.01020.15850.02490.02510.3743-0.20330.03180.1367-0.08040.01480.1093-0.00060.0323-7.7701-2.042425.2199
70.7974-0.4629-0.23210.7937-0.03250.4419-0.1858-0.1139-0.2070.21310.02220.270.1707-0.17660.16370.2299-0.1490.08860.2175-0.04270.2349-23.3747-8.316716.7461
80.94210.1679-0.26190.74870.3231.092-0.0514-0.01790.0309-0.07370.00250.16190.0934-0.27550.04890.0304-0.0474-0.01510.114-0.01040.0955-13.37563.71965.9795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 81
2X-RAY DIFFRACTION2A82 - 217
3X-RAY DIFFRACTION3A218 - 322
4X-RAY DIFFRACTION4A323 - 440
5X-RAY DIFFRACTION5B1 - 165
6X-RAY DIFFRACTION6B166 - 243
7X-RAY DIFFRACTION7B244 - 311
8X-RAY DIFFRACTION8B312 - 440

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