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- PDB-7qi9: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7qi9
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.2 in complex with UDP
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 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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 7.2 in complex with UDP
Authors: Silva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

Downloads & links

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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)71,1114
Polymers70,3022
Non-polymers8082
Water10,791599
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;166(5):474-483. doi:10.1099/mic.0.000898
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-33 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.619, 90.415, 95.509
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 DSM 44199 (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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M Potassium Sodium Tartrate pH 7.2, 20% 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: 1.23→50 Å / Num. obs: 171306 / % possible obs: 95.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.79 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Net I/σ(I): 15.1
Reflection shellResolution: 1.23→1.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13931 / Rpim(I) all: 0.357 / Rrim(I) all: 0.716 / % possible all: 80.5

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Processing

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

7qpc


Resolution: 1.23→48.4 Å / SU ML: 0.1073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.9628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1618 8578 5.01 %
Rwork0.1419 162564 -
obs0.1429 171142 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.23→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 50 599 4952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074649
X-RAY DIFFRACTIONf_angle_d0.93956400
X-RAY DIFFRACTIONf_chiral_restr0.072772
X-RAY DIFFRACTIONf_plane_restr0.0154829
X-RAY DIFFRACTIONf_dihedral_angle_d11.39661707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.240.25682030.23263975X-RAY DIFFRACTION70.91
1.24-1.260.23422780.22324393X-RAY DIFFRACTION78.6
1.26-1.270.24842760.20915074X-RAY DIFFRACTION89.98
1.27-1.290.23042670.20235192X-RAY DIFFRACTION92.1
1.29-1.310.21972960.20075194X-RAY DIFFRACTION92.75
1.31-1.320.22762830.21085293X-RAY DIFFRACTION93.57
1.32-1.340.21252580.18765305X-RAY DIFFRACTION93.83
1.34-1.360.19072640.17195320X-RAY DIFFRACTION94.6
1.36-1.390.18692620.16035405X-RAY DIFFRACTION94.91
1.39-1.410.19212760.14425392X-RAY DIFFRACTION95.13
1.41-1.430.17212830.13055403X-RAY DIFFRACTION95.9
1.43-1.460.14812850.12655482X-RAY DIFFRACTION96.86
1.46-1.490.16482740.12275476X-RAY DIFFRACTION96.96
1.49-1.520.15223130.12055466X-RAY DIFFRACTION97
1.52-1.550.15532990.12025502X-RAY DIFFRACTION97.38
1.55-1.590.15753040.12015536X-RAY DIFFRACTION97.56
1.59-1.630.15572820.12255528X-RAY DIFFRACTION97.58
1.63-1.670.15263110.1245455X-RAY DIFFRACTION96.7
1.67-1.720.15092870.1225545X-RAY DIFFRACTION97.85
1.72-1.770.13662800.11755589X-RAY DIFFRACTION97.75
1.77-1.840.14352930.11875585X-RAY DIFFRACTION98.03
1.84-1.910.13782680.12265599X-RAY DIFFRACTION98.42
1.91-20.14963120.13145627X-RAY DIFFRACTION98.67
2-2.10.14752920.12975607X-RAY DIFFRACTION98.3
2.1-2.230.14143080.12565653X-RAY DIFFRACTION98.86
2.24-2.410.13482810.12365699X-RAY DIFFRACTION99.24
2.41-2.650.13462870.13525746X-RAY DIFFRACTION99.44
2.65-3.030.17533120.14535716X-RAY DIFFRACTION99.28
3.03-3.820.15883060.15035832X-RAY DIFFRACTION99.74
3.82-48.40.18163380.16175975X-RAY DIFFRACTION99.14

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