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

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Basic information

Entry
Database: PDB / ID: 7pho
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 in complex with 4-hydroxybenzaldehyde
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
BICARBONATE ION / P-HYDROXYBENZALDEHYDE / D-MALATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsNunes-Costa, D. / Silva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221) Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 in complex with 4-hydroxybenzaldehyde
Authors: Nunes-Costa, D. / Silva, A. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 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)71,53613
Polymers70,3022
Non-polymers1,23411
Water8,161453
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 area5880 Å2
ΔGint-11 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.548, 90.542, 95.340
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 464 molecules

#2: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.15 M DL-Malic Acid pH 7.1; 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.268→65.654 Å / Num. obs: 161347 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 1.268→1.29 Å / Redundancy: 5 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8041 / CC1/2: 0.579 / Rpim(I) all: 0.552 / Rrim(I) all: 1.248 / % possible all: 100

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Processing

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

7p5l


Resolution: 1.27→65.65 Å / SU ML: 0.1329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1641 7947 4.93 %
Rwork0.145 153389 -
obs0.1459 161336 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.87 Å2
Refinement stepCycle: LAST / Resolution: 1.27→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 88 453 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764883
X-RAY DIFFRACTIONf_angle_d0.93156703
X-RAY DIFFRACTIONf_chiral_restr0.075804
X-RAY DIFFRACTIONf_plane_restr0.0147869
X-RAY DIFFRACTIONf_dihedral_angle_d11.22971867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.33372560.30275076X-RAY DIFFRACTION99.96
1.28-1.30.29722420.27115059X-RAY DIFFRACTION99.96
1.3-1.310.28112960.24165064X-RAY DIFFRACTION99.96
1.31-1.330.25862630.2275107X-RAY DIFFRACTION99.96
1.33-1.350.24462570.21775033X-RAY DIFFRACTION99.98
1.35-1.370.2282570.20775084X-RAY DIFFRACTION99.98
1.37-1.390.23232720.19835069X-RAY DIFFRACTION99.94
1.39-1.410.23022690.19165066X-RAY DIFFRACTION100
1.41-1.430.19462370.18335081X-RAY DIFFRACTION99.96
1.43-1.450.20652780.17615067X-RAY DIFFRACTION99.89
1.45-1.480.18422650.1645079X-RAY DIFFRACTION100
1.48-1.50.16692670.14535093X-RAY DIFFRACTION99.98
1.5-1.530.15142520.13955087X-RAY DIFFRACTION99.94
1.53-1.560.17693020.12825055X-RAY DIFFRACTION99.96
1.56-1.60.15092610.12135065X-RAY DIFFRACTION99.91
1.6-1.640.14512820.1165072X-RAY DIFFRACTION99.98
1.64-1.680.14882640.11715135X-RAY DIFFRACTION99.98
1.68-1.720.15182590.1195091X-RAY DIFFRACTION99.93
1.72-1.770.15962530.12385118X-RAY DIFFRACTION99.96
1.77-1.830.16312780.13165079X-RAY DIFFRACTION99.94
1.83-1.890.16082510.1335115X-RAY DIFFRACTION100
1.89-1.970.1422820.12645123X-RAY DIFFRACTION99.94
1.97-2.060.13692550.11595113X-RAY DIFFRACTION99.8
2.06-2.170.13192420.11825152X-RAY DIFFRACTION99.72
2.17-2.30.13222440.12055160X-RAY DIFFRACTION99.83
2.3-2.480.14172520.12565160X-RAY DIFFRACTION99.83
2.48-2.730.15382700.13765171X-RAY DIFFRACTION99.63
2.73-3.130.16882790.14735170X-RAY DIFFRACTION99.6
3.13-3.940.16632700.14765246X-RAY DIFFRACTION99.58
3.94-65.650.16982920.16495399X-RAY DIFFRACTION99.25

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