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- PDB-7p8g: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7p8g
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 - apo form
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homologyglucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / beta-D-glucopyranose / MALONATE ION / Glucosyl-3-phosphoglycerate synthase
Function and homology information
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 Tecnologia Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 - apo form
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,5757
Polymers35,1511
Non-polymers4246
Water1,54986
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,15014
Polymers70,3022
Non-polymers84812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area6650 Å2
ΔGint-97 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.423, 101.423, 122.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Glucosyl-3-phosphoglycerate synthase /


Mass: 35151.129 Da / Num. of mol.: 1
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 (E. coli)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 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: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.13→46.6 Å / Num. obs: 34136 / % possible obs: 98.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 46.03 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.056 / Net I/σ(I): 15
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 581 / Rpim(I) all: 0.276 / Rrim(I) all: 0.635 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P5L
Resolution: 2.13→46.6 Å / SU ML: 0.3063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 1714 5.03 %
Rwork0.2054 32342 -
obs0.2065 34056 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.38 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 23 86 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662354
X-RAY DIFFRACTIONf_angle_d0.91153214
X-RAY DIFFRACTIONf_chiral_restr0.0538392
X-RAY DIFFRACTIONf_plane_restr0.0099415
X-RAY DIFFRACTIONf_dihedral_angle_d13.2578865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.190.39731200.36082743X-RAY DIFFRACTION98.32
2.19-2.260.32821570.29082641X-RAY DIFFRACTION98.24
2.26-2.340.29361460.27012684X-RAY DIFFRACTION97.89
2.34-2.440.26281460.25332679X-RAY DIFFRACTION98.81
2.44-2.550.30541510.25212656X-RAY DIFFRACTION97.33
2.55-2.680.29511490.26232692X-RAY DIFFRACTION98.71
2.68-2.850.30461360.2622701X-RAY DIFFRACTION98.78
2.85-3.070.3061190.2572737X-RAY DIFFRACTION98.86
3.07-3.380.22981590.22872690X-RAY DIFFRACTION98.17
3.38-3.870.19161410.18962707X-RAY DIFFRACTION99.1
3.87-4.870.17751590.15022689X-RAY DIFFRACTION98.61
4.88-46.60.20161310.16922723X-RAY DIFFRACTION96.98

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