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- PDB-7p5l: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7p5l
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 - 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 / (2S)-2-hydroxybutanedioic acid / D-MALATE / Glucosyl-3-phosphoglycerate synthase
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsSilva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 - apo form
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 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
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5704
Polymers70,3022
Non-polymers2682
Water10,575587
1
B: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5704
Polymers70,3022
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_774-x+5/2,-y+2,z-1/21
Buried area2670 Å2
ΔGint-20 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.098, 90.605, 95.264
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 (E. coli)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


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


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.165 M DL-Malic Acid pH 7.1; 22% (w/v) 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: 1.22→50 Å / Num. obs: 182244 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.24 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 17739 / Rpim(I) all: 0.379 / Rrim(I) all: 0.734 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSJuly 4 2012data reduction
SCALA3.3.20data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+25 / Resolution: 1.22→48.23 Å / SU ML: 0.1086 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1638 9129 5.01 %
Rwork0.1431 173016 -
obs0.1441 182145 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.34 Å2
Refinement stepCycle: LAST / Resolution: 1.22→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 18 587 5000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914738
X-RAY DIFFRACTIONf_angle_d1.00776506
X-RAY DIFFRACTIONf_chiral_restr0.0779777
X-RAY DIFFRACTIONf_plane_restr0.0158855
X-RAY DIFFRACTIONf_dihedral_angle_d6.1467704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.230.26242950.23135726X-RAY DIFFRACTION99.59
1.23-1.250.22633070.20835730X-RAY DIFFRACTION99.75
1.25-1.260.2443140.20525680X-RAY DIFFRACTION99.68
1.26-1.280.22472920.20545728X-RAY DIFFRACTION99.6
1.28-1.30.23093050.19265692X-RAY DIFFRACTION99.27
1.3-1.310.21763030.20145688X-RAY DIFFRACTION99.72
1.31-1.330.21463210.18915735X-RAY DIFFRACTION99.9
1.33-1.350.18812910.17535707X-RAY DIFFRACTION99.78
1.35-1.370.19383020.16675741X-RAY DIFFRACTION99.92
1.37-1.40.18093050.15575732X-RAY DIFFRACTION99.92
1.4-1.420.18233130.1425741X-RAY DIFFRACTION99.8
1.42-1.450.15623050.13155697X-RAY DIFFRACTION99.78
1.45-1.470.15322940.13255762X-RAY DIFFRACTION99.95
1.47-1.50.16932840.13015707X-RAY DIFFRACTION99.09
1.5-1.540.16183150.12535773X-RAY DIFFRACTION99.9
1.54-1.570.15343060.12285726X-RAY DIFFRACTION99.93
1.57-1.610.15022860.12765772X-RAY DIFFRACTION99.92
1.61-1.660.15112900.12495776X-RAY DIFFRACTION99.97
1.66-1.70.14553350.12315731X-RAY DIFFRACTION99.9
1.7-1.760.14653150.12055732X-RAY DIFFRACTION99.82
1.76-1.820.13513200.11675777X-RAY DIFFRACTION99.8
1.82-1.90.13662790.12055768X-RAY DIFFRACTION99.39
1.9-1.980.14492990.12515786X-RAY DIFFRACTION99.84
1.98-2.090.15872980.12635838X-RAY DIFFRACTION99.9
2.09-2.220.14153140.12485789X-RAY DIFFRACTION99.82
2.22-2.390.14563260.12675793X-RAY DIFFRACTION99.71
2.39-2.630.15762850.13415840X-RAY DIFFRACTION99.58
2.63-3.010.15613270.14565820X-RAY DIFFRACTION99.34
3.01-3.790.15073090.14655910X-RAY DIFFRACTION99.66
3.79-48.230.19422940.16456119X-RAY DIFFRACTION99

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