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

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Basic information

Entry
Database: PDB / ID: 4kmi
TitleCrystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4
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
PHOSPHATE ION / 4-O-beta-D-mannosyl-D-glucose phosphorylase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)88,68510
Polymers87,8792
Non-polymers8068
Water16,934940
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)266,05630
Polymers263,6386
Non-polymers2,41924
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 area36290 Å2
ΔGint-358 kcal/mol
Surface area81110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.469, 82.469, 307.729
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-787-

HOH

21A-909-

HOH

31B-718-

HOH

41B-754-

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.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 46.33 %
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: 1.8→50 Å / Num. all: 72315 / Num. obs: 72284 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5 / Num. unique all: 7222 / % possible all: 100

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Processing

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

1vkd


Resolution: 1.8→35.472 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8484 / SU ML: 0.21 / σ(F): 1.97 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 3646 5.04 %RANDOM
Rwork0.1892 ---
obs0.1914 72274 99.95 %-
all-72310 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.1 Å2 / Biso mean: 14.2271 Å2 / Biso min: 3.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 46 940 7046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076250
X-RAY DIFFRACTIONf_angle_d1.1468492
X-RAY DIFFRACTIONf_chiral_restr0.079912
X-RAY DIFFRACTIONf_plane_restr0.0051094
X-RAY DIFFRACTIONf_dihedral_angle_d13.2442274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8003-1.8240.30571460.240126402786
1.824-1.8490.29361490.215326102759
1.849-1.87540.23631620.20226232785
1.8754-1.90340.23931350.197726142749
1.9034-1.93310.28121370.18926552792
1.9331-1.96480.24971580.186826422800
1.9648-1.99870.23941560.186126202776
1.9987-2.0350.21731380.175626112749
2.035-2.07420.22361400.167226632803
2.0742-2.11650.20631420.161426392781
2.1165-2.16250.24521350.17526702805
2.1625-2.21280.24611360.177526132749
2.2128-2.26820.22621340.176726542788
2.2682-2.32950.24151200.175526672787
2.3295-2.3980.23891400.180126172757
2.398-2.47540.25921360.188826562792
2.4754-2.56380.2541480.185726542802
2.5638-2.66650.24041440.19626412785
2.6665-2.78780.24561440.189726122756
2.7878-2.93470.21741610.195526342795
2.9347-3.11840.23271270.195426482775
3.1184-3.3590.24661260.188226472773
3.359-3.69680.19711340.181626622796
3.6968-4.23090.21480.177726212769
4.2309-5.32760.20631110.185526572768
5.3276-35.4790.25661390.241826582797

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