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- PDB-3wat: Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase ... -

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Basic information

Entry
Database: PDB / ID: 3wat
TitleCrystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with Man+Glc
Components4-O-beta-D-mannosyl-D-glucose phosphorylase
KeywordsTRANSFERASE / 5-bladed beta propeller fold / phosphorylase / mannan biodegradation
Function / homology
Function and homology information


4-O-beta-D-mannosyl-D-glucose phosphorylase / hexosyltransferase activity / cell wall organization / carbohydrate metabolic process
Similarity search - Function
4-O-beta-D-mannosyl-D-glucose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / beta-D-mannopyranose / PHOSPHATE ION / 4-O-beta-D-mannosyl-D-glucose phosphorylase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNakae, S. / Ito, S. / Higa, M. / Senoura, T. / Wasaki, J. / Hijikata, A. / Shionyu, M. / Ito, S. / Shirai, T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP
Authors: Nakae, S. / Ito, S. / Higa, M. / Senoura, T. / Wasaki, J. / Hijikata, A. / Shionyu, M. / Ito, S. / Shirai, T.
History
DepositionMay 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: 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

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Assembly

Deposited unit
A: 4-O-beta-D-mannosyl-D-glucose phosphorylase
B: 4-O-beta-D-mannosyl-D-glucose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,98010
Polymers87,8792
Non-polymers1,1018
Water24,4101355
1
A: 4-O-beta-D-mannosyl-D-glucose phosphorylase
B: 4-O-beta-D-mannosyl-D-glucose phosphorylase
hetero molecules

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase
B: 4-O-beta-D-mannosyl-D-glucose phosphorylase
hetero molecules

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase
B: 4-O-beta-D-mannosyl-D-glucose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,93930
Polymers263,6386
Non-polymers3,30224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38140 Å2
ΔGint-170 kcal/mol
Surface area80700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.540, 82.540, 307.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-719-

HOH

21A-800-

HOH

31A-948-

HOH

41B-690-

HOH

51B-710-

HOH

61B-1116-

HOH

71B-1169-

HOH

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Components

#1: Protein 4-O-beta-D-mannosyl-D-glucose phosphorylase / MGP / Mannosylglucose phosphorylase


Mass: 43939.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF0772 / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q5LH68, 4-O-beta-D-mannosyl-D-glucose phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 2.0M ammonium sulfate, 2.0M ammonium diphosphate, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→26.32 Å / Num. obs: 103109 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 6.02 Å2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.9 / Num. unique all: 15131 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKD

1vkd


Resolution: 1.6→25.623 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9212 / SU ML: 0.13 / σ(F): 2.03 / Phase error: 15.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 5153 5 %RANDOM
Rwork0.1623 ---
obs0.1629 103100 99.99 %-
all-103110 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.21 Å2 / Biso mean: 10.5935 Å2 / Biso min: -0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 68 1355 7595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076392
X-RAY DIFFRACTIONf_angle_d1.1198688
X-RAY DIFFRACTIONf_chiral_restr0.079946
X-RAY DIFFRACTIONf_plane_restr0.0051118
X-RAY DIFFRACTIONf_dihedral_angle_d13.0662344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.21491730.180333283501
1.6182-1.63720.21061460.178832323378
1.6372-1.65720.19381660.176733053471
1.6572-1.67820.17661650.171832623427
1.6782-1.70030.20151560.175432463402
1.7003-1.72350.17771710.164633013472
1.7235-1.74820.17461760.160132723448
1.7482-1.77430.16671710.157832203391
1.7743-1.8020.16881800.163732803460
1.802-1.83150.18591770.16332433420
1.8315-1.86310.18911470.160632823429
1.8631-1.89690.17441720.160932783450
1.8969-1.93340.1811850.1632163401
1.9334-1.97290.18351720.166432743446
1.9729-2.01580.16581610.167533293490
2.0158-2.06260.1761790.161632933472
2.0626-2.11420.16871810.145331713352
2.1142-2.17130.16991720.148833083480
2.1713-2.23520.15761730.156132433416
2.2352-2.30730.15161780.147732603438
2.3073-2.38970.16821620.159732793441
2.3897-2.48530.2041750.164332123387
2.4853-2.59830.16821830.168533113494
2.5983-2.73510.21231790.172932143393
2.7351-2.90630.17261790.172632643443
2.9063-3.13030.17931650.171332943459
3.1303-3.44470.15541680.159632573425
3.4447-3.94150.15631760.148332633439
3.9415-4.960.16421990.145332363435
4.96-25.62660.19531660.183632743440

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