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

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Basic information

Entry
Database: PDB / ID: 6dvv
Title2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD and Mn2+.
Components6-phospho-alpha-glucosidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phospho-alpha-glucosidase / NAD / Mn2+
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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 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 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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
Revision 1.2Oct 30, 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)102,77920
Polymers100,6692
Non-polymers2,10918
Water6,666370
1
A: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5338
Polymers50,3351
Non-polymers1,1997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,24512
Polymers50,3351
Non-polymers91011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.027, 86.027, 230.777
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-735-

HOH

21B-723-

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, 388 molecules

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


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM Mn; Screen: Classics II (G4), 0.2M Lithium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350;

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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: 47795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.036 / Rrim(I) all: 0.099 / Rsym value: 0.092 / Χ2: 1.525 / Net I/σ(I): 25.2
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2327 / CC1/2: 0.837 / Rpim(I) all: 0.324 / Rrim(I) all: 0.894 / Rsym value: 0.833 / Χ2: 0.991 / % possible all: 99.5

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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→28.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.533 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21896 2527 5.3 %RANDOM
Rwork0.16428 ---
obs0.16709 45255 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.294 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.81 Å20 Å2
2--1.63 Å20 Å2
3----5.27 Å2
Refinement stepCycle: 1 / Resolution: 2.25→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 118 370 7304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0147148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176376
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.79719
X-RAY DIFFRACTIONr_angle_other_deg0.4491.69814949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2265877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.63122.622370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.957151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7331543
X-RAY DIFFRACTIONr_chiral_restr0.0680.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.040.027991
X-RAY DIFFRACTIONr_gen_planes_other0.0370.021294
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_it2.4373.6353490
X-RAY DIFFRACTIONr_mcbond_other2.4343.6353489
X-RAY DIFFRACTIONr_mcangle_it3.6335.4424364
X-RAY DIFFRACTIONr_mcangle_other3.6335.4434365
X-RAY DIFFRACTIONr_scbond_it3.1424.0993658
X-RAY DIFFRACTIONr_scbond_other3.1384.0993658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7016.0015353
X-RAY DIFFRACTIONr_long_range_B_refined7.1244.3198111
X-RAY DIFFRACTIONr_long_range_B_other7.09844.0428050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 204 -
Rwork0.234 3247 -
obs--99.51 %
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)
12.7611.33720.11252.32251.22173.3373-0.0998-0.34980.27950.2145-0.0746-0.0844-0.37920.10470.17450.2556-0.0761-0.09940.1539-0.0760.157524.216822.191241.9152
20.7966-0.09930.06930.2797-0.56042.6196-0.0033-0.05440.00540.1073-0.0833-0.2268-0.20440.43480.08660.169-0.15-0.02280.1866-0.05680.330626.645521.50222.1087
31.14810.4933-0.38492.4546-0.16052.30530.1046-0.13990.30630.3866-0.11820.1874-0.61690.00830.01360.3904-0.07710.07310.0618-0.13180.35876.071936.942219.1618
40.5203-0.59280.38710.7431-1.11538.6565-0.1475-0.01230.25990.14860.0107-0.2485-0.340.08980.13690.3885-0.2088-0.08630.1531-0.06170.309329.531340.218931.7886
50.56540.15450.11620.56360.05891.4019-0.0145-0.03190.14570.0595-0.0243-0.155-0.25030.27850.03880.1315-0.10080.00630.0953-0.04850.293719.232523.111713.4677
64.86361.4183-1.69043.0291-0.96192.5172-0.1139-0.33430.51720.08090.14860.561-0.3559-0.7657-0.03460.10690.17250.03770.5328-0.18250.4086-32.576215.978120.9219
71.21960.1212-0.28923.37381.27282.5837-0.08640.1180.2195-0.167-0.04250.5006-0.0762-0.75440.12890.0271-0.0211-0.01750.3208-0.04080.2243-24.82153.64575.2499
80.94530.1835-0.19191.03050.3483.3339-0.055-0.1150.05640.14050.01890.0180.3251-0.33930.03610.128-0.08030.02620.1097-0.02670.1198-8.8478-1.321719.6962
94.4094-4.6566-3.10755.03393.68224.0423-0.3956-0.2388-0.43540.44780.13610.43930.6034-0.63480.25940.1635-0.20230.12560.48320.00240.3475-33.5207-5.024219.1702
101.02470.687-0.00731.58190.99922.3391-0.07970.02250.1355-0.1205-0.05270.2456-0.0216-0.48980.13240.0995-0.0552-0.00130.1567-0.02120.2382-12.26734.07975.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2A71 - 169
3X-RAY DIFFRACTION3A170 - 270
4X-RAY DIFFRACTION4A271 - 313
5X-RAY DIFFRACTION5A314 - 440
6X-RAY DIFFRACTION6B1 - 85
7X-RAY DIFFRACTION7B86 - 143
8X-RAY DIFFRACTION8B144 - 269
9X-RAY DIFFRACTION9B270 - 316
10X-RAY DIFFRACTION10B317 - 440

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