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- PDB-3qhp: Crystal structure of the catalytic domain of cholesterol-alpha-gl... -

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Basic information

Entry
Database: PDB / ID: 3qhp
TitleCrystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori
ComponentsType 1 capsular polysaccharide biosynthesis protein J (CapJ)
KeywordsTRANSFERASE / Rossmann Fold / glycosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
: / 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
Type 1 capsular polysaccharide biosynthesis protein J (CapJ)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsLee, S.J. / Lee, B.I. / Suh, S.W.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori
Authors: Lee, S.J. / Lee, B.I. / Suh, S.W.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 1 capsular polysaccharide biosynthesis protein J (CapJ)
B: Type 1 capsular polysaccharide biosynthesis protein J (CapJ)


Theoretical massNumber of molelcules
Total (without water)37,1572
Polymers37,1572
Non-polymers00
Water5,044280
1
A: Type 1 capsular polysaccharide biosynthesis protein J (CapJ)


Theoretical massNumber of molelcules
Total (without water)18,5781
Polymers18,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type 1 capsular polysaccharide biosynthesis protein J (CapJ)


Theoretical massNumber of molelcules
Total (without water)18,5781
Polymers18,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.786, 40.714, 53.738
Angle α, β, γ (deg.)101.44, 94.87, 90.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Type 1 capsular polysaccharide biosynthesis protein J (CapJ) / cholesterol-alpha-glucosyltransferase


Mass: 18578.461 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 201-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 26695 / Gene: HP0421 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O25175
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350, 0.1M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.9194, 0.9196, 0.9062
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 23, 2008
ADSC QUANTUM 3152CCDNov 28, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91941
30.91961
40.90621
ReflectionResolution: 1.5→20 Å / Num. obs: 45557 / % possible obs: 96 %
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.138 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→19.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.368 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22734 2306 5.1 %RANDOM
Rwork0.196 ---
obs0.19757 43082 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.71 Å2 / Biso mean: 17.49 Å2 / Biso min: 3.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.12 Å2-0.27 Å2
2---0.11 Å2-0.62 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 0 280 2720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9823454
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65825.437103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.811510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211847
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7661.51592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41322571
X-RAY DIFFRACTIONr_scbond_it2.0123960
X-RAY DIFFRACTIONr_scangle_it3.4084.5877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 158 -
Rwork0.231 3076 -
all-3234 -
obs--93.5 %

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