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- PDB-2x60: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 2x60
TitleCrystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP.
ComponentsMANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEOTIDYL TRANSFERASE
Function / homology
Function and homology information


mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding / metal ion binding
Similarity search - Function
: / : / : / MannoseP isomerase/GMP-like beta-helix domain / Nucleotidyl transferase domain / Nucleotidyl transferase / 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'-TRIPHOSPHATE / mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase and its Regulation by Divalent Ions.
Authors: Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y.
History
DepositionFeb 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
B: MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4066
Polymers77,3112
Non-polymers1,0954
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-42.1 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.926, 79.567, 70.952
Angle α, β, γ (deg.)90.00, 107.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE / GDP-MANNOSE PYROPHOSPHORYLASE


Mass: 38655.359 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: DSM 3109 / Plasmid: PMH1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ORIGAMI (DE3) PLYSS
References: UniProt: Q9X0C3, mannose-1-phosphate guanylyltransferase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 261 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 261 TO LEU ENGINEERED RESIDUE IN CHAIN B, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN B, VAL 261 TO LEU

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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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 5
Details: 100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 200 MM CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→67.6 Å / Num. obs: 17147 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5S

2x5s


Resolution: 2.8→67.57 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 41.34 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26697 1007 5.9 %RANDOM
Rwork0.20737 ---
obs0.21104 16126 98.72 %-
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: 74.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å23.16 Å2
2--3.56 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 66 19 5465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225581
X-RAY DIFFRACTIONr_bond_other_d0.0010.023885
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9887564
X-RAY DIFFRACTIONr_angle_other_deg0.81339513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41524.718248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.371151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4141528
X-RAY DIFFRACTIONr_chiral_restr0.0680.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
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_it0.2791.53336
X-RAY DIFFRACTIONr_mcbond_other0.0491.51330
X-RAY DIFFRACTIONr_mcangle_it0.53325438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.85732245
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4624.52126
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 72 -
Rwork0.284 1185 -
obs--98.67 %
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)
17.2334-0.6134-2.98182.5905-0.60583.96610.20120.1230.70220.64440.070.0716-0.75330.0178-0.27120.39980.0002-0.05850.0744-0.06060.2619-0.1108-9.1728-18.6606
23.7632-0.2061-1.66413.11751.61315.78-0.1912-0.4334-0.56170.95040.00280.02120.5436-0.07610.18840.4967-0.0537-0.02790.19290.02890.3398-5.8991-25.286-12.3493
39.97121.6134-6.10161.0118-0.91835.0824-0.47140.2569-0.49480.1661-0.01470.19650.155-0.02490.4860.1936-0.0435-0.02870.0356-0.00920.359414.1402-21.7789-32.2394
411.4092-0.7716-3.15391.09670.26693.13470.1640.93051.4659-0.81310.0544-0.2957-0.2837-0.2611-0.21840.6911-0.09650.03760.51440.25240.51948.7985-12.4972-52.6188
58.55220.0089-1.78024.7620.88686.8315-0.58071.8233-1.0983-0.91330.21790.08711.5339-0.74130.36280.736-0.28560.070.8705-0.25130.37653.9803-29.4985-55.7953
610.0055-2.2939-3.8062.67610.85572.1916-0.5195-0.2597-0.30420.0580.2777-0.02630.30410.30080.24180.1566-0.0366-0.11610.17770.110.250234.718-22.1454-36.4393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 93
2X-RAY DIFFRACTION2A94 - 251
3X-RAY DIFFRACTION3A252 - 333
4X-RAY DIFFRACTION4B1 - 93
5X-RAY DIFFRACTION5B94 - 251
6X-RAY DIFFRACTION6B252 - 333

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