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- PDB-3f1y: Mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus -

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Basic information

Entry
Database: PDB / ID: 3f1y
TitleMannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
ComponentsMannosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / GT-A type glycosyltransferase / GT-81 / mannosyl-3-phosphoglycerate synthase / Rubrobacter xylanophilus / GDP-mannose
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate synthase activity / glucosyl-3-phosphoglycerate synthase / metal ion binding
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
Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciessynthetic construct (others)
Rubrobacter xylanophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsMacedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N. / da Costa, M.S.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary crystallographic analysis of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
Authors: Sa-Moura, B. / Albuquerque, L. / Empadinhas, N. / da Costa, M.S. / Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
C: Mannosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2858
Polymers86,0952
Non-polymers1906
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-107 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.881, 108.881, 311.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Mannosyl-3-phosphoglycerate synthase / mannosyl/glucosyl-3-phosphoglycerate synthase


Mass: 43047.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Rubrobacter xylanophilus (bacteria)
Strain: DSM 9941 / Gene: mpgS / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: B7SY86, mannosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, 2M NaCl, 100mM NaH2PO4, 100mM KH2PO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→77.8 Å / Num. all: 56613 / Num. obs: 56613 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.4 % / Biso Wilson estimate: 41.41 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 1.2 / Num. unique all: 8094 / Rsym value: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→51.394 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.28 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2711 5.08 %Random
Rwork0.188 50674 --
obs0.1895 53385 94.6 %-
all-53385 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.555 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 134.56 Å2 / Biso mean: 56.755 Å2 / Biso min: 33.05 Å2
Baniso -1Baniso -2Baniso -3
1-9.621 Å20 Å2-0 Å2
2--9.621 Å20 Å2
3----19.242 Å2
Refine analyzeLuzzati d res low obs: 51.4 Å / Luzzati sigma a obs: 0.2793 Å
Refinement stepCycle: LAST / Resolution: 2.2→51.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 6 424 5365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135035
X-RAY DIFFRACTIONf_angle_d1.4066830
X-RAY DIFFRACTIONf_dihedral_angle_d18.1761848
X-RAY DIFFRACTIONf_chiral_restr0.097749
X-RAY DIFFRACTIONf_plane_restr0.006914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.24010.30341350.25482265X-RAY DIFFRACTION83
2.2401-2.28320.23621220.23112350X-RAY DIFFRACTION85
2.2832-2.32980.27591330.24092378X-RAY DIFFRACTION86
2.3298-2.38040.26041110.21842456X-RAY DIFFRACTION88
2.3804-2.43580.22961620.20432511X-RAY DIFFRACTION92
2.4358-2.49670.25991510.20312524X-RAY DIFFRACTION92
2.4967-2.56420.29481420.21622576X-RAY DIFFRACTION94
2.5642-2.63970.25091260.21522631X-RAY DIFFRACTION93
2.6397-2.72490.26751490.21632639X-RAY DIFFRACTION95
2.7249-2.82230.22721210.21362696X-RAY DIFFRACTION97
2.8223-2.93520.25631360.21312738X-RAY DIFFRACTION97
2.9352-3.06880.26181390.21232748X-RAY DIFFRACTION98
3.0688-3.23060.22991480.20122779X-RAY DIFFRACTION99
3.2306-3.4330.21621590.1922790X-RAY DIFFRACTION99
3.433-3.69790.21231370.16422828X-RAY DIFFRACTION99
3.6979-4.06990.17731420.15222839X-RAY DIFFRACTION99
4.0699-4.65850.16471500.13872887X-RAY DIFFRACTION100
4.6585-5.86790.19311750.16852912X-RAY DIFFRACTION100
5.8679-51.40810.20841730.18853127X-RAY DIFFRACTION100
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)
11.4666-0.4837-0.80192.6630.4671.97520.06560.12830.1447-0.2429-0.06620.0976-0.572-0.3754-00.42060.2139-0.04320.5148-0.03960.3725-112.297177.19542.1597
20.59220.026-0.45583.26180.48641.18890.02610.0313-0.11920.0616-0.0945-0.0018-0.56970.0106-00.36650.1306-0.03060.6297-0.05970.3973-109.230271.7172.1838
30.9298-1.2699-0.39661.95730.89221.96210.03050.033-0.061-0.17730.0001-0.0952-0.3381-0.073900.34220.0517-0.01790.5386-0.06360.3765-101.47762.7896-3.3454
41.2403-0.4472-1.18020.52470.20510.7946-0.0891-0.53080.02410.09930.17030.05970.06830.2151-00.25850.0586-0.01550.6385-0.10290.4335-91.048653.4737.4249
52.9393-0.4656-0.17571.48910.6391.86130.052-0.11050.3251-0.14-0.028-0.2319-0.35010.218400.2823-0.14040.02060.4652-0.10060.4751-61.513157.7503-14.5362
61.05990.4895-0.47141.41610.47851.26650.03560.08670.1433-0.1844-0.0847-0.0732-0.42470.0546-00.3129-0.0177-0.00820.5656-0.10070.4877-68.013656.0422-15.48
72.3041-0.3514-0.58760.6114-0.00090.78830.12440.00790.0289-0.1331-0.0313-0.0275-0.19680.034200.2838-0.02340.01720.5295-0.09610.4305-78.657755.4662-9.9118
81.3995-1.0889-0.3241-0.78650.24030.69140.09790.313-0.2594-0.2094-0.0709-0.1104-0.1594-0.2093-00.4090.02850.01050.6512-0.09910.4899-93.548853.5701-19.2026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:103)A10 - 103
2X-RAY DIFFRACTION2(chain A and resid 104:178)A104 - 178
3X-RAY DIFFRACTION3(chain A and resid 179:285)A179 - 285
4X-RAY DIFFRACTION4(chain A and resid 286:334)A286 - 334
5X-RAY DIFFRACTION5(chain C and resid 9:102)C9 - 102
6X-RAY DIFFRACTION6(chain C and resid 103:180)C103 - 180
7X-RAY DIFFRACTION7(chain C and resid 181:278)C181 - 278
8X-RAY DIFFRACTION8(chain C and resid 279:333)C279 - 333

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