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- PDB-7pvl: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7pvl
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 - apo form
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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
Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSilva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 - apo form
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionOct 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyl-3-phosphoglycerate synthase
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4467
Polymers70,3022
Non-polymers1445
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability ...Evidence: gel filtration, Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures. Microbiology (Reading). 2020 May;166(5):474-483. doi: 10.1099/mic.0.000898. PMID: 32100712.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-51 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 89.909, 95.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 35151.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal KLAAALEHHHHHH sequence corresponds to a linker followed by an hexahistidine tag used for protein purification.
Source: (gene. exp.) Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 0.2 M MgCl2; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96112 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 113499 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.03 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 17
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10985 / Rpim(I) all: 0.407 / Rrim(I) all: 0.871 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P5L

7p5l


Resolution: 1.43→48.15 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1805 5679 5.01 %
Rwork0.1484 107735 -
obs0.15 113414 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.63 Å2
Refinement stepCycle: LAST / Resolution: 1.43→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 5 786 5223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484636
X-RAY DIFFRACTIONf_angle_d0.74046343
X-RAY DIFFRACTIONf_chiral_restr0.0703761
X-RAY DIFFRACTIONf_plane_restr0.0107823
X-RAY DIFFRACTIONf_dihedral_angle_d11.13351715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.26021980.22643520X-RAY DIFFRACTION99.04
1.45-1.460.26621830.21913528X-RAY DIFFRACTION99.92
1.46-1.480.25391920.20453536X-RAY DIFFRACTION100
1.48-1.50.25872020.20063554X-RAY DIFFRACTION99.95
1.5-1.520.24051800.20043557X-RAY DIFFRACTION99.95
1.52-1.540.25762080.1873538X-RAY DIFFRACTION99.97
1.54-1.560.2231700.17643566X-RAY DIFFRACTION99.92
1.56-1.590.21471760.15963583X-RAY DIFFRACTION99.92
1.59-1.610.19712090.15063551X-RAY DIFFRACTION100
1.61-1.640.22161850.14473551X-RAY DIFFRACTION99.95
1.64-1.670.18851980.13623550X-RAY DIFFRACTION100
1.67-1.70.17521660.12743598X-RAY DIFFRACTION100
1.7-1.730.18111920.12723574X-RAY DIFFRACTION100
1.73-1.760.20461820.13873549X-RAY DIFFRACTION99.95
1.76-1.80.18811880.13813583X-RAY DIFFRACTION100
1.8-1.840.17591790.14473583X-RAY DIFFRACTION99.97
1.84-1.890.19171870.14973582X-RAY DIFFRACTION99.95
1.89-1.940.19211910.13773572X-RAY DIFFRACTION99.97
1.94-20.15321800.13323588X-RAY DIFFRACTION100
2-2.060.17131750.12823580X-RAY DIFFRACTION100
2.06-2.140.15462100.12853586X-RAY DIFFRACTION99.97
2.14-2.220.16961920.13133611X-RAY DIFFRACTION100
2.22-2.320.1721900.13133585X-RAY DIFFRACTION99.97
2.32-2.450.15381810.13693634X-RAY DIFFRACTION99.92
2.45-2.60.17681870.13963597X-RAY DIFFRACTION100
2.6-2.80.1491950.15213630X-RAY DIFFRACTION99.97
2.8-3.080.19021660.15343659X-RAY DIFFRACTION100
3.08-3.530.1692070.14693647X-RAY DIFFRACTION99.92
3.53-4.440.15031980.13833694X-RAY DIFFRACTION99.92
4.44-48.150.20152120.17183849X-RAY DIFFRACTION99.85

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