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- PDB-2wvl: Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB... -

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Basic information

Entry
Database: PDB / ID: 2wvl
TitleMannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in complex with GDP-alpha-D-Mannose and Mg(II)
ComponentsMANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE
KeywordsTRANSFERASE / GT-A FOLD / GLYCOSYLTRANSFERASE / RETAINING MECHANISM / GLUCOSYL TRANSFERASE
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate synthase activity / mannosylglycerate biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / metal ion binding / 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-phosphogylcerate synthase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.806 Å
AuthorsGoncalves, S. / Borges, N. / Esteves, A.M. / Victor, B. / Soares, C.M. / Santos, H. / Matias, P.M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural Analysis of Thermus Thermophilus Hb27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight Into the Retaining Mechanism of Glycosyltransferases.
Authors: Goncalves, S. / Borges, N. / Esteves, A.M. / Victor, B. / Soares, C.M. / Santos, H. / Matias, P.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Analysis of Mannosyl-3-Phosphoglycerate Synthase from Thermus Thermophilus Hb27
Authors: Goncalves, S. / Borges, N. / Santos, H. / Matias, P.M.
History
DepositionOct 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 19, 2014Group: Database references / Source and taxonomy
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,88811
Polymers87,3022
Non-polymers1,5869
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-173.9 kcal/mol
Surface area30910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.456, 113.456, 195.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 6
2114B1 - 6
1216A7 - 8
2216B7 - 8
1314A9 - 30
2314B9 - 30
1416A31 - 39
2416B31 - 39
1515A40 - 42
2515B40 - 42
1614A43 - 87
2614B43 - 87
1715A88 - 90
2715B88 - 90
1814A91 - 117
2814B91 - 117
1916A118 - 134
2916B118 - 134
11014A135 - 140
21014B135 - 140
11116A141 - 143
21116B141 - 143
11214A144 - 202
21214B144 - 202
11316A203 - 211
21316B203 - 211
11416A212 - 216
21416B212 - 216
11515A217 - 223
21515B217 - 223
11614A224 - 288
21614B224 - 288
11715A289 - 296
21715B289 - 296
11814A297 - 308
21814B297 - 308
11916A309 - 318
21916B309 - 318
12015A319 - 338
22015B319 - 338
12114A339 - 351
22114B339 - 351
12215A352 - 361
22215B352 - 361
12314A362 - 369
22314B362 - 369
12415A370 - 391
22415B370 - 391

NCS oper: (Code: given
Matrix: (0.92058, -0.39055, -0.00117), (-0.39055, -0.92058, 0.00036), (-0.00122, 0.00013, -1)
Vector: 10.53314, 51.67445, 49.42385)

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Components

#1: Protein MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE


Mass: 43650.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA
References: UniProt: Q72K30, 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 65.7 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2 AS AN ADDITIVE, CO-CRYSTALLIZED WITH 1-5 MM GDP-ALPHA-D-MANNOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0672
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0672 Å / Relative weight: 1
ReflectionResolution: 2.8→45.1 Å / Num. obs: 32332 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.62
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 1.23 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXCDEphasing
SHARPphasing
REFMAC5.5.0088refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.806→45.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 30.799 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23396 1620 5.1 %RANDOM
Rwork0.1727 ---
obs0.17579 30259 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.293 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.11 Å2
Refinement stepCycle: LAST / Resolution: 2.806→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 85 36 6147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9968473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48322.694297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.362151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521568
X-RAY DIFFRACTIONr_chiral_restr0.1030.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214778
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_it0.7771.51417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53122267
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7133875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6084.5834
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2361medium positional0.360.5
2B2361medium positional0.360.5
1A637loose positional1.052.5
2B637loose positional1.052.5
1A2361medium thermal7.752
2B2361medium thermal7.752
1A637loose thermal9.338
2B637loose thermal9.338
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 115 -
Rwork0.339 2142 -
obs--97.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28661.1346-0.11124.30.95645.49790.02920.18510.0952-0.25550.0393-0.6763-0.5850.9206-0.06860.085-0.06480.06390.21730.07950.2116109.73124.87325.543
21.1807-0.4456-0.38243.77151.68565.2222-0.1487-0.1139-0.220.40130.0788-0.36321.01850.45520.06990.24160.03360.04280.15830.03280.1862101.644-14.17523.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 391
2X-RAY DIFFRACTION1A400
3X-RAY DIFFRACTION2B1 - 391
4X-RAY DIFFRACTION2B400

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