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- PDB-7fip: The native structure of beta-1,2-mannobiose phosphorylase from Th... -

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Basic information

Entry
Database: PDB / ID: 7fip
TitleThe native structure of beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.
ComponentsBeta-1,2-mannobiose phosphorylase
KeywordsTRANSFERASE / Mannobiose / phosphorylase / thermoanaerobacter / crystallization / complex structure
Function / homology
Function and homology information


beta-1,2-mannobiose phosphorylase / GDP-mannose biosynthetic process / glycosyltransferase activity
Similarity search - Function
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-1,2-mannobiose phosphorylase
Similarity search - Component
Biological speciesThermoanaerobacter sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,47420
Polymers143,4284
Non-polymers1,04716
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-564 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.317, 206.317, 78.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 10 mM ZnCl2, 26% 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: Oct 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.39→35.4 Å / Num. obs: 127183 / % possible obs: 99.9 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shellResolution: 2.39→2.43 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3164

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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: 2.39→35.38 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 3895 3.06 %
Rwork0.1872 123288 -
obs0.1888 127183 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.14 Å2 / Biso mean: 34.4252 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 2.39→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9940 0 16 913 10869
Biso mean--54.09 34.6 -
Num. residues----1209
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 (%)
2.39-2.420.3171420.270744204562100
2.42-2.450.34151410.27424425456699
2.45-2.480.3191360.27343794515100
2.48-2.520.31651400.259644624602100
2.52-2.550.33081380.25624370450899
2.55-2.590.29131320.256244134545100
2.59-2.630.3621400.24924389452999
2.63-2.670.32921400.245243884528100
2.67-2.720.28671400.22674418455899
2.72-2.770.28381410.222643554496100
2.77-2.820.33141480.22314452460099
2.82-2.880.24971360.216444424578100
2.88-2.940.28781380.21284429456799
2.94-3.010.24651360.21144354571100
3.01-3.090.30931420.220143524494100
3.09-3.170.25991400.20454421456199
3.17-3.260.25961440.20034381452599
3.26-3.370.24841400.188644344574100
3.37-3.490.23281320.18684424455699
3.49-3.630.23811360.18284365450199
3.63-3.790.20271410.17394413455499
3.79-3.990.18631440.16594428457299
3.99-4.240.21091390.14914343448299
4.24-4.570.19561410.13484381452299
4.57-5.030.17981400.13544381452199
5.03-5.750.14641420.139243904532100
5.75-7.240.22791270.151544584585100
7.24-35.380.20111390.1644340447998

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