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- PDB-7fiq: The crystal structure of mannose-bound beta-1,2-mannobiose phosph... -

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Basic information

Entry
Database: PDB / ID: 7fiq
TitleThe crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.
ComponentsBeta-1,2-mannobiose phosphorylase
KeywordsTRANSFERASE / Mannobiose / phosphorylase / thermoanaerobacter / crystallization / complex structure
Function / homologybeta-1,2-mannobiose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / GDP-mannose biosynthetic process / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / alpha-D-mannopyranose / TRIETHYLENE GLYCOL / Beta-1,2-mannobiose phosphorylase
Function and homology information
Biological speciesThermoanaerobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsDai, L. / Chang, Z. / Yang, J. / Liu, W. / Yang, Y. / Chen, C.-C. / Zhang, L. / Huang, J. / Sun, Y. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFC2100300 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural investigation of a thermostable 1,2-beta-mannobiose phosphorylase from Thermoanaerobacter sp. X-514.
Authors: Dai, L. / Chang, Z. / Yang, J. / Liu, W. / Yang, Y. / Chen, C.C. / Zhang, L. / Huang, J.W. / Sun, Y. / Guo, R.T.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-1,2-mannobiose phosphorylase
B: Beta-1,2-mannobiose phosphorylase
A: Beta-1,2-mannobiose phosphorylase
D: Beta-1,2-mannobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,89129
Polymers143,4284
Non-polymers2,46325
Water24,0861337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-505 kcal/mol
Surface area46630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.195, 203.195, 77.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein / Sugars , 2 types, 8 molecules CBAD

#1: Protein
Beta-1,2-mannobiose phosphorylase / Beta-1 / 2-mannobiose:phosphate alpha-D-mannosyltransferase


Mass: 35856.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. (strain X514) (bacteria)
Strain: X514 / Gene: Teth514_1789 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B0K2C3, beta-1,2-mannobiose phosphorylase
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1358 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1337 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 10 mM ZnCl2, 24% PEG3350, 180 mM Tris-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.22→34.9 Å / Num. obs: 150222 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.134 / Net I/σ(I): 9
Reflection shellResolution: 2.22→2.25 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3065

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
SAINTdata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5b0r

5b0r


Resolution: 2.22→34.85 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 3829 2.55 %
Rwork0.1727 146390 -
obs0.1739 150219 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.85 Å2 / Biso mean: 24.8869 Å2 / Biso min: 3.69 Å2
Refinement stepCycle: final / Resolution: 2.22→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9940 0 107 1337 11384
Biso mean--33.31 30.87 -
Num. residues----1208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.250.26491200.26224574469483
2.25-2.280.2961270.25994745487286
2.28-2.310.31041360.25564901503788
2.31-2.340.27141310.24935074520591
2.34-2.380.27961400.23735208534894
2.38-2.410.29761440.21535476562098
2.41-2.450.29041460.217854995645100
2.45-2.50.25351460.217355705716100
2.5-2.540.26021450.203555565701100
2.54-2.590.26691520.204755515703100
2.59-2.640.22511380.202155125650100
2.64-2.70.27051490.188455965745100
2.7-2.760.23161380.182455595697100
2.76-2.830.25761470.182554815628100
2.83-2.910.23221440.18655875731100
2.91-2.990.24221520.189955665718100
2.99-3.090.27611380.19255085646100
3.09-3.20.21131480.169655435691100
3.2-3.330.22951460.170355545700100
3.33-3.480.20391390.158355145653100
3.48-3.660.19021400.140355635703100
3.66-3.890.19051540.144155625716100
3.89-4.190.15441440.133254885632100
4.19-4.610.17021470.121255915738100
4.62-5.280.15891340.125655145648100
5.28-6.640.18921430.149855795722100
6.65-34.850.21651410.18025519566099

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