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- PDB-2jjm: Crystal Structure of a family GT4 glycosyltransferase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 2jjm
TitleCrystal Structure of a family GT4 glycosyltransferase from Bacillus anthracis ORF BA1558.
ComponentsGLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
KeywordsTRANSFERASE / GLYCOSYL TRANSFER / GLYCOSYLTRANSFERASE / ANTHRAX / NUCLEOTIDE / CARBOHYDRATE
Function / homology
Function and homology information


bacillithiol biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / nucleotide binding
Similarity search - Function
N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA / : / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-D-glucosaminyl L-malate synthase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsRuane, K.M. / Davies, G.J. / Martinez-Fleites, C.
CitationJournal: Proteins / Year: 2008
Title: Crystal Structure of a Family Gt4 Glycosyltransferase from Bacillus Anthracis Orf Ba1558.
Authors: Ruane, K.M. / Davies, G.J. / Martinez-Fleites, C.
History
DepositionApr 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
B: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
C: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
D: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
E: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
F: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
G: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
H: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
I: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
J: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
K: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
L: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)534,78112
Polymers534,78112
Non-polymers00
Water00
1
A: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
B: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
C: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
D: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)178,2604
Polymers178,2604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-110.3 kcal/mol
Surface area65750 Å2
MethodPQS
2
E: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
F: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
G: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
H: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)178,2604
Polymers178,2604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-94.3 kcal/mol
Surface area65760 Å2
MethodPQS
3
I: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
J: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
K: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN
L: GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)178,2604
Polymers178,2604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-86.8 kcal/mol
Surface area66090 Å2
MethodPQS
Unit cell
Length a, b, c (Å)134.597, 204.667, 135.329
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.01812, 0.80901, -0.58751), (0.7975, -0.34272, -0.49653), (-0.60305, -0.47754, -0.63898)-122.52144, 224.76289, 100.91868
2given(-0.99592, -0.05967, -0.06775), (-0.05528, -0.19035, 0.98016), (-0.07138, 0.9799, 0.18628)-60.03427, 121.70748, -104.01926
3given(0.01327, -0.73439, 0.6786), (-0.73768, -0.46534, -0.48917), (0.67502, -0.4941, -0.54792)39.00619, 186.51832, 144.73512
4given(0.06681, 0.60038, 0.79692), (0.69334, 0.54643, -0.46979), (-0.71751, 0.58392, -0.37976)-63.69684, 43.38068, -72.81827
5given(0.00296, -0.54544, -0.83815), (0.7106, 0.59086, -0.382), (0.70359, -0.59446, 0.38934)144.86177, 34.89108, 106.93374
6given(0.07341, -0.70649, -0.70391), (-0.71301, -0.53068, 0.45826), (-0.6973, 0.46825, -0.54269)164.18539, 104.19109, -51.02093
7given(-0.14585, 0.66949, 0.72836), (-0.68381, -0.60027, 0.41482), (0.71494, -0.43756, 0.54535)-77.60213, 115.84541, 80.75996
8given(0.99669, 0.07933, -0.01781), (0.02578, -0.10055, 0.9946), (0.07711, -0.99176, -0.10226)56.48273, 114.374, 189.57652
9given(0.05313, 0.77428, -0.63061), (-0.68883, -0.42879, -0.58451), (-0.72297, 0.46544, 0.51056)-47.58692, 188.89807, -54.43936
10given(-0.99756, -0.06797, 0.01612), (-0.06624, 0.99368, 0.09057), (-0.02218, 0.08928, -0.99576)4.30745, -2.73487, 74.0854
11given(-0.045, -0.77086, 0.63541), (0.75509, -0.4427, -0.48359), (0.65408, 0.45803, 0.60199)109.59505, 237.86994, -8.27642

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Components

#1: Protein
GLYCOSYL TRANSFERASE, GROUP 1 FAMILY PROTEIN / GLYCOSYL TRANSFERASE


Mass: 44565.074 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: PETYSBLIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q81ST7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.5 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH 7.5, 0.2M NA2SO4, 14% PEG 3350

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 117619 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 100.415 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.1→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2903911.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: BULK SOLVENT MODEL USED DISORDERED REGIONS ARE THE SAME IN EACH MONOMER AND ARE 12- 13 43-46 61- 64 196-198
RfactorNum. reflection% reflectionSelection details
Rfree0.262 5887 5 %RANDOM
Rwork0.254 ---
obs0.254 117109 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.263 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 91.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.18 Å20 Å2-7.36 Å2
2--5.56 Å20 Å2
3---2.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33924 0 0 0 33924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 943 4.9 %
Rwork0.349 18370 -
obs--97.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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