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- PDB-2zu7: Crystal structure of mannosyl-3-phosphoglycerate synthase from Py... -

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Basic information

Entry
Database: PDB / ID: 2zu7
TitleCrystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii
ComponentsMannosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / GT-A fold / glycosyltransferase / GT55 / 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
Mannosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,9562
Polymers91,9562
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-8 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.075, 86.923, 83.328
Angle α, β, γ (deg.)90.00, 101.78, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 30% MPD, 0.05M sodium acetate, 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: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26230 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 25.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 2404 / Rsym value: 0.144 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1588512.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1295 5.1 %RANDOM
Rwork0.21 ---
obs0.21 25216 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.9615 Å2 / ksol: 0.300717 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--18.96 Å20 Å2-1.31 Å2
2--37.81 Å20 Å2
3----18.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 0 35 5880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.492
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_scangle_it2.292.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 202 5.6 %
Rwork0.268 3421 -
obs-3421 82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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