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- PDB-2y4m: MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH GDP-Mannose -

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Basic information

Entry
Database: PDB / ID: 2y4m
TitleMANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH GDP-Mannose
ComponentsMANNOSYLGLYCERATE SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GT FAMILY 78 MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE / GDP-MANNOSE
Function / homology
Function and homology information


: / : / Mannosylglycerate synthase C-terminal domain / Mannosylglycerate synthase, GT domain / 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
Chem-GDX / Mannosylglycerate synthase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Davis, B.G. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.
Authors: Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Dumon, C. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
History
DepositionJan 7, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 2, 2011ID: 2XW5
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,11817
Polymers89,2012
Non-polymers1,91715
Water2,918162
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A: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71411
Polymers44,6011
Non-polymers1,11410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4046
Polymers44,6011
Non-polymers8035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.500, 149.500, 154.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MANNOSYLGLYCERATE SYNTHASE / MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE


Mass: 44600.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-382 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. / Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: DSM 4252 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER
References: UniProt: D0MI02, mannosyl-3-phosphoglycerate synthase

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Non-polymers , 5 types, 177 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDX / GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER


Mass: 619.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23N5O17P2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 201 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 202 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 202 TO ALA
Nonpolymer detailsETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYOPROTECTANT GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYOPROTECTANT GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER (GDX): GDP-MANNOSE IS THE SUGAR DONOR SUBSTRATE FOR MGS CHLORIDE (CL): CHLORIDE OCCUPIES THE POSITION OF THE SUGAR ACCEPTOR OF MGS
Sequence detailsC-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ...C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ENTROPY MINIMIZATION.

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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: 5.58 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growpH: 5
Details: 4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE, PH 5.5, 0.3 M MAGNESIUM FORMATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2009 / Details: OSMIC VARIMAX HF MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→23.4 Å / Num. obs: 47729 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 47.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO7

2bo7


Resolution: 2.7→129.47 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.432 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21878 2704 5.1 %RANDOM
Rwork0.19136 ---
obs0.19279 47729 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→129.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6189 0 118 162 6469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9528878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82222.266331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.646151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.491565
X-RAY DIFFRACTIONr_chiral_restr0.1020.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215039
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7671.53791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51926122
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23332725
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7914.52751
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 210 -
Rwork0.32 3774 -
obs--98.71 %

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