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- PDB-3o3p: Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose -

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Basic information

Entry
Database: PDB / ID: 3o3p
TitleCrystal structure of R. xylanophilus MpgS in complex with GDP-Mannose
ComponentsMannosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / GTA / GT-81 family / dinucleotide-binding fold / Glucosyltransferase / mannosylglycerate biosynthesis / GDP-mannose / GDP-glucose / MpgS / GpgS
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate synthase activity / glucosyl-3-phosphoglycerate synthase
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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 / GUANOSINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesRubrobacter xylanophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.529 Å
AuthorsMacedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N. / da Costa, M.S.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity
Authors: Empadinhas, N. / Pereira, P.J.B. / Albuquerque, L. / Costa, J. / Sa-Moura, B. / Marques, A.T. / Macedo-Ribeiro, S. / da Costa, M.S.
History
DepositionJul 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_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_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: Mannosyl-3-phosphoglycerate synthase
B: Mannosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2638
Polymers86,0952
Non-polymers1,1686
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-43 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.370, 108.370, 311.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mannosyl-3-phosphoglycerate synthase /


Mass: 43047.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubrobacter xylanophilus (bacteria) / Strain: DSM 9941 / NBRC 16129 / Plasmid: pET30a / Production host: Escherichia coli (E. coli)
References: UniProt: B7SY86, mannosyl-3-phosphoglycerate synthase

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / Guanosine diphosphate mannose


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE N-TERMINAL SEQUENCE MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEF CORRESPONDS TO THE ...THE N-TERMINAL SEQUENCE MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEF CORRESPONDS TO THE EXPRESSION TAG AND LINKER.

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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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 2M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.529→69.67 Å / Num. obs: 37299 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 41.62 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.3 / Num. measured all: 254012
Reflection shellResolution: 2.529→2.67 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 0.218 / Num. unique all: 5300 / Rsym value: 0.526 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1Y

3f1y


Resolution: 2.529→54.185 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.43 / σ(F): 0.01 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1805 4.97 %random
Rwork0.1883 34495 --
obs0.1904 36300 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.864 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 171.46 Å2 / Biso mean: 45.201 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.9722 Å20 Å2-0 Å2
2--4.9722 Å20 Å2
3----9.9444 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.529→54.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4959 0 71 130 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135154
X-RAY DIFFRACTIONf_angle_d1.097011
X-RAY DIFFRACTIONf_dihedral_angle_d16.9731983
X-RAY DIFFRACTIONf_chiral_restr0.073763
X-RAY DIFFRACTIONf_plane_restr0.005924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.529-2.59740.31361190.24392427X-RAY DIFFRACTION91
2.5974-2.67380.29311300.2222463X-RAY DIFFRACTION93
2.6738-2.76010.26611370.20482563X-RAY DIFFRACTION96
2.7601-2.85880.26091170.19242606X-RAY DIFFRACTION97
2.8588-2.97320.23611450.17962573X-RAY DIFFRACTION98
2.9732-3.10850.24241200.18452656X-RAY DIFFRACTION98
3.1085-3.27240.19411540.1712621X-RAY DIFFRACTION98
3.2724-3.47740.21031480.16792653X-RAY DIFFRACTION99
3.4774-3.74580.17731090.14822725X-RAY DIFFRACTION99
3.7458-4.12260.20391530.14382696X-RAY DIFFRACTION100
4.1226-4.71890.16661460.13242761X-RAY DIFFRACTION100
4.7189-5.94410.21610.16372769X-RAY DIFFRACTION100
5.9441-54.19740.2131660.18172982X-RAY DIFFRACTION99
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)
11.4984-0.553-0.33830.7510.50680.96120.2979-0.6595-0.281.0301-0.5109-0.8095-0.72540.7287-0.0060.5176-0.3237-0.18720.54530.07660.32462.6564-20.462311.4339
22.73970.0770.58124.1897-1.1241.59730.0675-0.00080.0986-0.1313-0.19550.0302-0.4254-0.0069-0.0010.2041-0.10390.00580.22130.08710.135653.4232-18.9409-10.5003
31.78620.9932-0.20293.3121-0.21362.01420.0916-0.18630.09120.4611-0.199-0.0709-0.35170.3517-00.2434-0.1287-0.07390.2840.06830.15151.223-27.32385.6261
44.2098-0.1219-0.80620.8093-0.08211.82650.00460.18080.1681-0.08640.1243-0.0162-0.0698-0.1120.00030.0894-0.0246-0.02110.20570.10190.226637.1239-38.1725-4.692
51.27681.07180.04311.4212-0.5430.8326-0.23880.6029-0.0312-0.23320.11230.28610.1464-0.1427-0.00420.13180.0632-0.03420.41720.14630.31485.3841-42.28481.0876
61.9177-0.3086-0.14032.6278-0.2662.08710.0743-0.12640.48930.2823-0.1355-0.0108-0.68940.00530.00010.2609-0.02470.06730.29410.03270.333110.4588-34.133122.9723
74.02180.0591-0.48681.2888-0.25781.65910.1595-0.08790.30370.0489-0.12540.1295-0.31790.02860.00020.07840.01670.03060.22080.09310.187818.4477-38.70157.3138
81.94412.3493-0.30782.8911-0.69282.17260.1874-0.5801-0.15430.5199-0.1187-0.028-0.49060.50790.00030.2876-0.08830.01120.39820.08730.243236.9411-38.604317.7556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:42)A10 - 42
2X-RAY DIFFRACTION2(chain A and resid 43:143)A43 - 143
3X-RAY DIFFRACTION3(chain A and resid 144:255)A144 - 255
4X-RAY DIFFRACTION4(chain A and resid 256:334)A256 - 334
5X-RAY DIFFRACTION5(chain B and resid 10:42)B10 - 42
6X-RAY DIFFRACTION6(chain B and resid 43:143)B43 - 143
7X-RAY DIFFRACTION7(chain B and resid 144:258)B144 - 258
8X-RAY DIFFRACTION8(chain B and resid 259:333)B259 - 333

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