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- PDB-2x65: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 2x65
TitleCrystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with mannose-1-phosphate.
ComponentsMANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding
Similarity search - Function
: / 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
1-O-phosphono-alpha-D-mannopyranose / PHOSPHATE ION / Mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
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)78,56512
Polymers77,3112
Non-polymers1,25510
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-79.2 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.933, 91.738, 69.730
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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(DE30 PLYSS)
References: UniProt: Q9X0C3, mannose-1-phosphate guanylyltransferase
#2: Sugar ChemComp-M1P / 1-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE 1-PHOSPHATE / 1-O-phosphono-alpha-D-mannose / 1-O-phosphono-D-mannose / 1-O-phosphono-mannose / Mannose 1-phosphate


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 170 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growDetails: 35% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→65.2 Å / Num. obs: 43388 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8

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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: 2.1→65.21 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.709 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1352 3.1 %RANDOM
Rwork0.187 ---
obs0.18837 42013 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-0 Å21.25 Å2
2--1.65 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 79 162 5659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023958
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.997613
X-RAY DIFFRACTIONr_angle_other_deg0.84339690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24124.683252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.593151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3721530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021078
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_it0.61.53348
X-RAY DIFFRACTIONr_mcbond_other0.1351.51332
X-RAY DIFFRACTIONr_mcangle_it1.10125466
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75432276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7734.52145
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 90 -
Rwork0.287 3117 -
obs--98.8 %
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)
15.49630.8054-1.07672.8405-0.69252.5158-0.01260.49950.6114-0.19340.02850.2418-0.2109-0.1043-0.01590.11490.0348-0.04240.05960.04760.1428-2.016125.05319.0343
24.92251.3036-1.68082.6083-0.78353.06750.4397-1.09080.65640.7173-0.33670.1603-0.48450.2656-0.1030.2774-0.11310.02250.2519-0.14520.1012-54.432412.563852.6432
33.0297-0.7533-0.63743.43960.07553.98740.03080.5944-0.6756-0.4856-0.22910.25530.48030.00890.19830.13720.0408-0.01060.1696-0.12010.15734.92536.223813.8927
44.57351.3794-1.32794.2297-0.6312.6744-0.0665-0.1347-0.77470.1039-0.07470.01820.4288-0.05370.14120.0832-0.01890.00570.01140.02510.1508-61.778-4.889843.705
55.49010.4892-2.1730.5892-0.20251.71040.08770.68930.022-0.25330.04220.1681-0.1297-0.2232-0.12990.14430.0049-0.05120.1049-0.02760.1149-10.54214.250518.2204
65.98761.7574-2.29991.7642-0.91771.87280.191-0.799-0.28690.4156-0.2681-0.1447-0.05950.33120.07710.1253-0.0309-0.05550.10860.03120.0943-45.99533.593146.1648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2B1 - 100
3X-RAY DIFFRACTION3A101 - 199
4X-RAY DIFFRACTION4B101 - 199
5X-RAY DIFFRACTION5A200 - 334
6X-RAY DIFFRACTION6B200 - 334

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