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- PDB-2bo4: Dissection of mannosylglycerate synthase: an archetypal mannosylt... -

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Basic information

Entry
Database: PDB / ID: 2bo4
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
CITRATE ANION / Mannosylglycerate synthase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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 Mannosylglyceerate 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 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,25312
Polymers277,1196
Non-polymers1,1356
Water31,8331767
1
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
E: MANNOSYLGLYCERATE SYNTHASE
F: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5028
Polymers184,7464
Non-polymers7564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
hetero molecules

C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5028
Polymers184,7464
Non-polymers7564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)261.148, 151.288, 153.240
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MANNOSYLGLYCERATE SYNTHASE /


Mass: 46186.473 Da / Num. of mol.: 6
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-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1767 / 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: 5.5 Å3/Da / Density % sol: 79 %
Crystal growDetails: 0.3 M TRI-SODIUM CITRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 40% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9783
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 432716 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 90

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Processing

Software
NameVersionClassification
HKLdata reduction
HKLdata scaling
SHELXphasing
SOLVEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.453 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 20759 5 %RANDOM
Rwork0.176 ---
obs0.177 392971 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18824 0 78 1767 20669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02119446
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217436
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.93326460
X-RAY DIFFRACTIONr_angle_other_deg0.851340128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48252274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1780.22796
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221744
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024446
X-RAY DIFFRACTIONr_nbd_refined0.2070.24009
X-RAY DIFFRACTIONr_nbd_other0.2430.220840
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.211160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.21533
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5351.511388
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.076218414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78538058
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9624.58046
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
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 1249
Rwork0.275 23933
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)
11.13590.1479-0.47821.0220.38471.0427-0.06440.0817-0.12270.0630.0266-0.11790.08540.07420.03780.0955-0.0860.02340.10850.01750.062686.1671-0.989835.1529
21.48520.5324-0.3191.29610.16540.6475-0.07480.02540.06910.03550.02380.21840.0418-0.09830.05110.1624-0.00210.03710.0274-0.01050.052459.7564-0.262174.895
31.1248-0.1619-0.08131.0427-0.61211.05840.07090.00870.1636-0.0176-0.1076-0.0541-0.10180.03990.03670.02880.0526-0.02870.16680.00220.0704108.253634.476-15.9409
41.7035-0.42360.05031.0485-0.41080.63060.03360.0257-0.21650.0407-0.0893-0.05460.06850.08580.05570.0589-0.063-0.00330.13920.03270.0685120.728511.607323.9655
50.8553-0.0280.56581.2267-0.22621.1328-0.06480.0568-0.0350.07610.0218-0.16240.00790.11060.0430.1678-0.03750.01420.02520.02520.058163.5362-39.646967.1681
60.84970.08740.30031.9827-0.21730.6353-0.02520.08010.14610.0569-0.0210.1781-0.1064-0.01810.04620.0651-0.0654-0.02780.13170.0220.059450.3554-17.476527.1062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 382
2X-RAY DIFFRACTION2B2 - 381
3X-RAY DIFFRACTION3C2 - 382
4X-RAY DIFFRACTION4D2 - 381
5X-RAY DIFFRACTION5E2 - 381
6X-RAY DIFFRACTION6F2 - 381

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