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- PDB-3pnn: The crystal structure of a glycosyltransferase from Porphyromonas... -

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Basic information

Entry
Database: PDB / ID: 3pnn
TitleThe crystal structure of a glycosyltransferase from Porphyromonas gingivalis W83
ComponentsConserved domain protein
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / alpha/beta/alpha Rossmann fold-like / formation of the glycosidic linkage / cytoplasmic
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / Conserved domain protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a glycosyltransferase from Porphyromonas gingivalis W83
Authors: Tan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Other
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8667
Polymers34,3141
Non-polymers5536
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.038, 109.038, 124.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

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Components

#1: Protein Conserved domain protein / glycosyltransferase


Mass: 34313.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0160 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7MXL4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Sodium Citrate Tribasic, 0.1M Sodium Cacodylate:HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→44.2 Å / Num. all: 34856 / Num. obs: 34856 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 43.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1711 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→44.153 Å / SU ML: 0.14 / σ(F): 0.01 / σ(I): 0 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1684 5.01 %random
Rwork0.1658 ---
obs0.1667 33637 96.11 %-
all-33637 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.466 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6781 Å20 Å20 Å2
2---3.6781 Å2-0 Å2
3---7.3563 Å2
Refinement stepCycle: LAST / Resolution: 1.901→44.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 36 203 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082510
X-RAY DIFFRACTIONf_angle_d1.0783386
X-RAY DIFFRACTIONf_dihedral_angle_d17.039937
X-RAY DIFFRACTIONf_chiral_restr0.073357
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.96860.2221450.18012804X-RAY DIFFRACTION86
1.9686-2.04750.2041410.16733059X-RAY DIFFRACTION93
2.0475-2.14070.19421540.16323070X-RAY DIFFRACTION94
2.1407-2.25350.18611750.16343130X-RAY DIFFRACTION96
2.2535-2.39470.18941800.16393195X-RAY DIFFRACTION97
2.3947-2.57960.19751960.17043186X-RAY DIFFRACTION98
2.5796-2.83910.18661500.17983293X-RAY DIFFRACTION99
2.8391-3.24980.18651890.17333314X-RAY DIFFRACTION99
3.2498-4.0940.17051860.15353352X-RAY DIFFRACTION99
4.094-44.16480.17381680.16273550X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -10.0518 Å / Origin y: 34.9385 Å / Origin z: 13.3354 Å
111213212223313233
T0.2512 Å20.006 Å20.0063 Å2-0.2265 Å2-0.01 Å2--0.2662 Å2
L1.8264 °2-0.1165 °2-0.1852 °2-0.4333 °2-0.2768 °2--0.9893 °2
S-0 Å °0.0494 Å °-0.2592 Å °-0.0669 Å °-0.0156 Å °-0.0016 Å °0.1216 Å °0.017 Å °0.0168 Å °
Refinement TLS groupSelection details: chain A

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