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- PDB-2bo8: DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLT... -

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Basic information

Entry
Database: PDB / ID: 2bo8
TitleDISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE
ComponentsMANNOSYLGLYCERATE SYNTHASE
KeywordsTRANSFERASE / CATALYSIS / GLYCOSYLTRANSFERASE / MANNOSE / STEREOSELECTIVITY
Function / homology
Function and homology information


mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / identical protein binding / metal ion binding
Similarity search - Function
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFlint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2005
Title: Structural dissection and high-throughput screening of mannosylglycerate synthase.
Authors: Flint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
History
DepositionApr 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / database_PDB_caveat ...citation / database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.method_details
Revision 1.4Dec 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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
C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
E: MANNOSYLGLYCERATE SYNTHASE
F: MANNOSYLGLYCERATE SYNTHASE
G: MANNOSYLGLYCERATE SYNTHASE
H: MANNOSYLGLYCERATE SYNTHASE
I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,96240
Polymers461,86510
Non-polymers7,09730
Water5,549308
1
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,58516
Polymers184,7464
Non-polymers2,83912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-164 kcal/mol
Surface area51730 Å2
MethodPISA
2
E: MANNOSYLGLYCERATE SYNTHASE
F: MANNOSYLGLYCERATE SYNTHASE
G: MANNOSYLGLYCERATE SYNTHASE
H: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,58516
Polymers184,7464
Non-polymers2,83912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-161 kcal/mol
Surface area51770 Å2
MethodPISA
3
I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules

I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,58516
Polymers184,7464
Non-polymers2,83912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area14220 Å2
ΔGint-164 kcal/mol
Surface area51560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)405.094, 161.430, 108.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MN / End label comp-ID: MN / Refine code: 1 / Auth seq-ID: 2 - 500 / Label seq-ID: 2

Dom-IDAuth asym-IDLabel asym-ID
1AA - L
2BB - O
3CC - R
4DD - U
5EE - X
6FF - AA
7GG - DA
8HH - GA
9II - JA
10JJ - MA

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Components

#1: Protein
MANNOSYLGLYCERATE SYNTHASE /


Mass: 46186.473 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (DE3)
References: UniProt: Q9RFR0, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-GDX / GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER


Mass: 619.325 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H23N5O17P2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growDetails: 10 MM NACL, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 15% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 175257 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKLdata reduction
HKLdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO6

2bo6


Resolution: 2.8→74.12 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 23.342 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 8687 5.1 %RANDOM
Rwork0.195 ---
obs0.196 162631 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31380 0 410 308 32098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02132710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.95444590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43653790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07622.1761700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53155180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.41915350
X-RAY DIFFRACTIONr_chiral_restr0.1430.24760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.215837
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.222368
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4760.2159
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5891.519240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.016230650
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.564315430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4534.513940
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3178 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.130.05
2Btight positional0.110.05
3Ctight positional0.080.05
4Dtight positional0.090.05
5Etight positional0.080.05
6Ftight positional0.050.05
7Gtight positional0.090.05
8Htight positional0.060.05
9Itight positional0.070.05
10Jtight positional0.090.05
1Atight thermal0.370.5
2Btight thermal0.360.5
3Ctight thermal0.190.5
4Dtight thermal0.190.5
5Etight thermal0.190.5
6Ftight thermal0.140.5
7Gtight thermal0.240.5
8Htight thermal0.160.5
9Itight thermal0.190.5
10Jtight thermal0.260.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 652
Rwork0.292 11987

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