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- PDB-2zu8: Crystal structure of mannosyl-3-phosphoglycerate synthase from Py... -

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Basic information

Entry
Database: PDB / ID: 2zu8
TitleCrystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii
ComponentsMannosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / GT-A fold / glycosyltransferase / GT55 / GDP-MANNOSE / Cytoplasm / Magnesium
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate synthase / mannosyl-3-phosphoglycerate synthase activity / mannosylglycerate biosynthetic process / cytoplasm
Similarity search - Function
Mannosyl-3-phosphoglycerate synthase / Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth) / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / Mannosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKawamura, T. / Watanabe, N. / Tanaka, I.
CitationJournal: To be Published
Title: Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii
Authors: Kawamura, T. / Watanabe, N. / Tanaka, I.
History
DepositionOct 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannosyl-3-phosphoglycerate synthase
B: Mannosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1674
Polymers91,9562
Non-polymers1,2112
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-38 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.238, 84.993, 83.592
Angle α, β, γ (deg.)90.00, 101.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mannosyl-3-phosphoglycerate synthase / MPG synthase / MPGS


Mass: 45977.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0927 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: O58689, mannosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 30% MPD, 0.05M sodium acetate, 0.1mM GDP-mannose, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2007
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27663 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 6.6 Å2 / Rsym value: 0.126 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 7.5 / Rsym value: 0.245 / % possible all: 81.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZU7

2zu7


Resolution: 2.4→42.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1908905.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1401 5.1 %RANDOM
Rwork0.226 ---
obs0.226 27650 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.6219 Å2 / ksol: 0.308517 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--5.54 Å20 Å2-2.72 Å2
2--15.19 Å20 Å2
3----9.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5972 0 78 0 6050
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.861.5
X-RAY DIFFRACTIONc_mcangle_it1.512
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 190 5 %
Rwork0.307 3585 -
obs--78.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3LIGAND:GDD.paramLIGAND:GDD.top

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