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- PDB-2x5s: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 2x5s
TitleCrystal structure of T. maritima GDP-mannose pyrophosphorylase in apo state.
ComponentsMANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEOTIDYL TRANSFERASE
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
Mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 10, 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 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...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 / struct_sheet
Item: _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


Theoretical massNumber of molelcules
Total (without water)77,3112
Polymers77,3112
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19.4 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.011, 92.999, 69.687
Angle α, β, γ (deg.)90.00, 110.25, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.43 Å3/Da / Density % sol: 49.47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 MM PCB PH 7.5, 35% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.35→65.37 Å / Num. obs: 31744 / % possible obs: 99.2 % / Observed criterion σ(I): 3.5 / Redundancy: 6 % / Biso Wilson estimate: 59.338 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CU2

2cu2


Resolution: 2.35→65.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 23.518 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.278 / 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
Rfree0.27315 1602 5 %RANDOM
Rwork0.22385 ---
obs0.22648 30129 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.786 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å20 Å21.18 Å2
2--4.94 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.35→65.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 0 47 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225487
X-RAY DIFFRACTIONr_bond_other_d0.0020.023845
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9737421
X-RAY DIFFRACTIONr_angle_other_deg0.78739412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13324.694245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.661151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4521528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
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_it0.4161.53330
X-RAY DIFFRACTIONr_mcbond_other0.0731.51328
X-RAY DIFFRACTIONr_mcangle_it0.79725422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.21732157
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0084.51999
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 114 -
Rwork0.368 2096 -
obs--93.45 %
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)
17.09550.6942-1.42983.5447-1.58886.16290.02250.4830.6877-0.26790.04590.0613-0.3939-0.2499-0.06840.1992-0.02280.01330.05240.01220.29079.659527.9465-12.9762
26.64461.3235-3.48881.9056-0.89776.20510.6572-1.94550.89860.7232-0.31520.0983-0.45331.0584-0.3420.3412-0.1640.04920.5919-0.30260.3372-42.973215.277921.078
33.576-2.1711-0.24784.5024-0.05457.52820.16020.4888-0.9183-0.5703-0.23330.44181.078-0.11050.07310.3348-0.0010.03150.1772-0.07460.365816.90638.7244-16.6478
46.78743.2191-3.29846.6772-1.41685.4736-0.5112-0.349-0.9492-0.25860.2206-0.50360.90120.48110.29060.19690.02310.04640.13650.00470.2069-50.5721-1.692210.6978
59.13051.1362-3.81161.4234-1.10763.4389-0.06750.81090.1988-0.39870.15260.0269-0.1448-0.2831-0.08510.2276-0.0463-0.02980.0863-0.00960.21111.20116.8127-13.5974
69.54482.429-3.93221.7434-0.93572.68070.1235-1.6237-0.23550.4799-0.3947-0.0675-0.0250.55480.27110.19780.01-0.02530.3867-0.00160.1597-34.76596.239914.3435
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 - 333
6X-RAY DIFFRACTION6B200 - 333

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