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- PDB-2x5z: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 2x5z
TitleCrystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GDP-mannose.
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'-DIPHOSPHATE-ALPHA-D-MANNOSE / mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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_conn.ptnr2_label_seq_id / _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)78,5465
Polymers77,3112
Non-polymers1,2353
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-47.2 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.227, 96.035, 217.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 20 MM CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24606 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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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: 2.7→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 24.474 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.096 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24415 1257 5.1 %RANDOM
Rwork0.19111 ---
obs0.19374 23310 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0 Å2
2---0.72 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5396 0 79 38 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225602
X-RAY DIFFRACTIONr_bond_other_d0.0010.023922
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9937590
X-RAY DIFFRACTIONr_angle_other_deg0.85939610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77224.758248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.921151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1551528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021076
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_it0.5411.53332
X-RAY DIFFRACTIONr_mcbond_other0.1011.51326
X-RAY DIFFRACTIONr_mcangle_it1.05225438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63432270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7374.52152
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 104 -
Rwork0.248 1708 -
obs--99.83 %
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)
11.86030.1056-1.83182.59210.93246.610.50120.04420.4729-0.2969-0.28080.4984-0.7992-0.6313-0.22040.31510.00190.12080.14670.00210.422614.225117.29029.2101
22.59910.1041-0.20264.1632.25565.67070.5048-0.04960.1478-0.05380.1627-0.5037-0.22240.8211-0.66750.1859-0.11510.11920.2105-0.11970.302631.362910.966310.6005
38.22335.616-1.92046.7228-0.34793.62660.3823-0.42520.25560.4625-0.51360.14980.1612-0.23330.13120.218-0.16060.08310.1776-0.05830.20048.0262.717127.5353
45.8412.0542-4.47142.6622-1.42217.57210.8751-0.51921.21370.38970.06810.6359-1.69870.1481-0.94310.6459-0.29470.33830.4566-0.17210.6585-27.2704-13.787344.1371
55.76410.338-3.00592.28430.93968.86230.1702-1.7272-0.210.63760.01670.09010.10421.4117-0.18690.4321-0.30410.1010.87210.01280.2834-20.306-28.776352.5334
67.45236.4548-3.33428.4135-3.76243.05230.444-0.53640.12260.5815-0.39020.3648-0.26790.0625-0.05390.3213-0.25970.15970.322-0.19640.2484-6.3771-12.039331.744
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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