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- PDB-7fis: The crystal structure of beta-1,2-mannobiose phosphorylase in com... -

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Basic information

Entry
Database: PDB / ID: 7fis
TitleThe crystal structure of beta-1,2-mannobiose phosphorylase in complex with mannose 1-phosphate (M1P)
ComponentsBeta-1,2-mannobiose phosphorylase
KeywordsTRANSFERASE / Mannobiose / thermoanaerobacter / mannose 1-phosphate
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 / 1-O-phosphono-alpha-D-mannopyranose / Beta-1,2-mannobiose phosphorylase
Function and homology information
Biological speciesThermoanaerobacter sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 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)146,55930
Polymers143,4284
Non-polymers3,13126
Water21,4561191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-557 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.959, 204.959, 78.482
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, 9 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-M1P / 1-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE 1-PHOSPHATE / 1-O-phosphono-alpha-D-mannose / 1-O-phosphono-D-mannose / 1-O-phosphono-mannose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Manp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 1212 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1191 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
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 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.16→35.15 Å / Num. obs: 163537 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6
Reflection shellResolution: 2.19→2.22 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3249

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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: 2.19→35.15 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 3893 2.38 %
Rwork0.1766 159644 -
obs0.1777 163537 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.46 Å2 / Biso mean: 27.3606 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: final / Resolution: 2.19→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9940 0 145 1191 11276
Biso mean--40.78 33.34 -
Num. residues----1208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.220.36931280.285445557395
2.22-2.240.27831410.26145607574897
2.24-2.270.33551330.253256715804100
2.27-2.310.28771380.2475706584498
2.31-2.340.26281310.24275646577799
2.34-2.370.28141400.243457115851100
2.37-2.410.31441400.233456925832100
2.41-2.450.30631380.225557185856100
2.45-2.490.261460.22657445890100
2.49-2.540.26611400.215857375877100
2.54-2.590.27961400.217156855825100
2.59-2.640.3061340.211557465880100
2.64-2.70.26121450.212657245869100
2.7-2.760.2821400.207456595799100
2.76-2.830.29381380.214557595897100
2.83-2.90.25441390.20457485887100
2.9-2.990.26481370.186556805817100
2.99-3.090.22251450.184857495894100
3.09-3.20.21261390.174757285867100
3.2-3.320.19931400.160657265866100
3.32-3.480.20791380.145257685906100
3.48-3.660.18581380.141757165854100
3.66-3.890.1841460.138356935839100
3.89-4.190.16151410.130657395880100
4.19-4.610.16491460.121257355881100
4.61-5.270.16331340.121357195853100
5.27-6.640.18911440.154757485892100
6.64-35.150.18971340.18395645577999

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