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- PDB-6vc6: 2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-gluc... -

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Basic information

Entry
Database: PDB / ID: 6vc6
Title2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+
Components6-phospho-alpha-glucosidase
KeywordsHYDROLASE / 6-phospho-alpha-glucosidase / Gut Microorganisms
Function / homology6-O-phosphono-alpha-D-glucopyranose / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesMerdibacter massiliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.133 Å
AuthorsWu, R. / Kim, Y. / Endres, M. / Joachimiak, J.
CitationJournal: To Be Published
Title: 2.1 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Mn2+
Authors: Wu, R. / Kim, Y. / Endres, M. / Joachimiak, A.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: 6-phospho-alpha-glucosidase
D: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,17419
Polymers206,9834
Non-polymers4,19015
Water10,719595
1
A: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7244
Polymers51,7461
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8165
Polymers51,7461
Non-polymers1,0714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9096
Polymers51,7461
Non-polymers1,1635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 6-phospho-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7244
Polymers51,7461
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.460, 62.257, 160.706
Angle α, β, γ (deg.)90.000, 90.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
6-phospho-alpha-glucosidase


Mass: 51745.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Merdibacter massiliensis (bacteria) / Gene: AGLB / Plasmid: PLASMID / Details (production host): pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: maltose-6'-phosphate glucosidase
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 606 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.6M Sodium Chloride, 0.1M MES:NaOH, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 106570 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.58 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Rrim(I) all: 0.135 / Χ2: 1.363 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.184.30.63452390.7420.3340.720.52198.3
2.18-2.224.60.56352790.8120.2850.6340.54599
2.22-2.264.90.53452310.8390.2610.5960.5799.4
2.26-2.314.90.44153420.8850.2170.4940.59799.9
2.31-2.364.90.39152920.910.1920.4370.62599.7
2.36-2.414.90.34653290.9250.1710.3880.66399.7
2.41-2.474.80.32752990.9180.1630.3670.68599.7
2.47-2.544.80.27852950.9370.1390.3120.74899.6
2.54-2.614.70.24852990.9460.1250.2790.82798.7
2.61-2.74.50.20853000.9580.1080.2350.90898.8
2.7-2.7950.18952670.9710.0910.2110.95999.7
2.79-2.950.17353490.9730.0840.1931.06199.8
2.9-3.044.90.1553480.9780.0730.1671.18299.8
3.04-3.24.90.13553580.980.0670.1511.40999.6
3.2-3.44.70.12353170.9810.0620.1381.72799.3
3.4-3.664.70.10753520.9860.0530.1212.05799
3.66-4.0350.10153410.9860.050.1132.29899.9
4.03-4.614.90.09654020.9860.0480.1072.56799.7
4.61-5.814.70.09953790.9850.050.1122.9198.8
5.81-504.70.10355520.9830.0530.1164.23899.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DVV

6dvv


Resolution: 2.133→48.614 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2286 5313 4.99 %
Rwork0.1961 --
obs0.1977 106528 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.27 Å2 / Biso mean: 49.0368 Å2 / Biso min: 26.55 Å2
Refinement stepCycle: final / Resolution: 2.133→48.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14131 0 262 595 14988
Biso mean--47.38 48.31 -
Num. residues----1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414725
X-RAY DIFFRACTIONf_angle_d0.77219930
X-RAY DIFFRACTIONf_chiral_restr0.0512098
X-RAY DIFFRACTIONf_plane_restr0.0052588
X-RAY DIFFRACTIONf_dihedral_angle_d25.5045577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.133-2.15710.32111510.2989292486
2.1571-2.18250.31451570.2848330298
2.1825-2.20910.2982110.2698337099
2.2091-2.23710.32891820.27123342100
2.2371-2.26650.31851540.2713340199
2.2665-2.29760.32711690.25423379100
2.2976-2.33040.26871590.25153388100
2.3304-2.36520.29272030.24663349100
2.3652-2.40210.30671940.24493348100
2.4021-2.44150.3091430.24053409100
2.4415-2.48360.27251770.24143426100
2.4836-2.52880.29981710.23693313100
2.5288-2.57740.30091820.2347338499
2.5774-2.630.29431620.232334898
2.63-2.68720.27781880.2337338298
2.6872-2.74970.28381900.23013352100
2.7497-2.81850.25761860.22383404100
2.8185-2.89470.27061950.22673315100
2.8947-2.97980.26221710.21833436100
2.9798-3.0760.27311670.22923423100
3.076-3.18590.24581680.22223389100
3.1859-3.31340.25431640.22053412100
3.3134-3.46420.25411700.2045336798
3.4642-3.64680.20811780.18393432100
3.6468-3.87520.20881870.17123394100
3.8752-4.17420.18772130.1553381100
4.1742-4.5940.17411840.14553425100
4.594-5.25810.17721940.1481339198
5.2581-6.6220.21651590.18773490100
6.622-48.6140.16671840.1653353998

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