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- PDB-3kia: Crystal structure of mannosyl-3-phosphoglycerate synthase from Ru... -

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Basic information

Entry
Database: PDB / ID: 3kia
TitleCrystal structure of mannosyl-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 / Glycosyltransferase
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
GUANOSINE-5'-MONOPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciessynthetic construct (others)
Rubrobacter xylanophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionNov 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
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_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_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_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)87,00110
Polymers86,0952
Non-polymers9068
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-43 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.010, 109.010, 313.418
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


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: 266117 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: B7SY86, mannosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES pH 6.0, 2.0M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→90.5 Å / Num. all: 27781 / Num. obs: 27781 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 53.51 Å2 / Rsym value: 0.061 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.31

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3f1y

3f1y


Resolution: 2.8→53.699 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 0 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1380 5.01 %
Rwork0.1899 26151 -
obs0.1924 27531 97.93 %
all-27348 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.995 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 145.22 Å2 / Biso mean: 53.9491 Å2 / Biso min: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.403 Å2-0 Å2-0 Å2
2--6.403 Å20 Å2
3----12.8061 Å2
Refinement stepCycle: LAST / Resolution: 2.8→53.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 54 106 5015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095018
X-RAY DIFFRACTIONf_angle_d0.9146812
X-RAY DIFFRACTIONf_dihedral_angle_d16.8531907
X-RAY DIFFRACTIONf_chiral_restr0.319744
X-RAY DIFFRACTIONf_plane_restr0.004898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.39171100.30082500X-RAY DIFFRACTION96
2.9001-3.01620.32591420.2332507X-RAY DIFFRACTION97
3.0162-3.15340.25341170.22482557X-RAY DIFFRACTION97
3.1534-3.31970.26031530.20322539X-RAY DIFFRACTION98
3.3197-3.52760.26551400.20562589X-RAY DIFFRACTION98
3.5276-3.79990.21161190.18472621X-RAY DIFFRACTION99
3.7999-4.18220.22831360.16822642X-RAY DIFFRACTION99
4.1822-4.7870.21231430.15082645X-RAY DIFFRACTION99
4.787-6.02990.21991570.17892708X-RAY DIFFRACTION99
6.0299-53.70890.22421630.1942843X-RAY DIFFRACTION98
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)
12.0568-0.25410.53342.8846-0.08670.29960.0295-0.11090.00940.0728-0.1356-0.1859-0.27930.21590.12010.2282-0.1934-0.03230.3770.1510.202955.379-19.2559-2.7283
21.00890.33540.15851.6910.16330.1590.1602-0.0464-0.11380.4702-0.3812-0.0696-0.20820.21280.18770.3761-0.1269-0.05240.50690.12980.269949.5585-30.28394.7665
31.15191.1908-0.53591.253-0.02310.8375-0.02540.37810.1744-0.15390.0263-0.17390.01460.0528-0.0080.2281-0.01480.03850.39910.15040.291333.3445-38.7192-3.362
43.01032.177-0.54813.49440.64731.07810.74830.3431.16790.0245-0.66130.42270.2754-0.4752-0.31610.2098-0.00420.09790.36380.12590.366957.1086-38.5692-12.2387
50.85050.2547-0.22151.6822-0.54521.14010.08830.12620.12740.0426-0.01530.3048-0.1978-0.1872-0.10790.2120.07530.05940.39710.10140.35529.7941-36.597614.3093
61.50570.8759-0.5760.349-0.2740.72890.2003-0.0494-0.16240.1012-0.14520.0595-0.1088-0.0222-0.03830.24180.01290.03570.4310.13930.300424.1492-40.84729.8886
70.92580.29590.09580.38020.39081.40730.293-0.2180.2702-0.2474-0.28760.2877-0.4931-0.0967-0.06990.6372-0.1620.01250.53370.09990.395543.075-32.342319.6277
80.1053-0.34460.07721.79130.0233.32920.02980.0552-0.19840.1419-0.0104-0.31720.30130.80740.16860.2778-0.04630.04380.5470.21780.42420.96-51.348524.1714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 14:179)
2X-RAY DIFFRACTION2(chain A and resid 180:255)
3X-RAY DIFFRACTION3(chain A and resid 256:322)
4X-RAY DIFFRACTION4(chain A and resid 323:333)
5X-RAY DIFFRACTION5(chain C and resid 9:186)
6X-RAY DIFFRACTION6(chain C and resid 187:285)
7X-RAY DIFFRACTION7(chain C and resid 286:321)
8X-RAY DIFFRACTION8(chain C and resid 322:333)

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