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- PDB-4m98: Acetyltransferase domain of PglB from Neisseria gonorrhoeae FA1090 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4m98
TitleAcetyltransferase domain of PglB from Neisseria gonorrhoeae FA1090
ComponentsPilin glycosylation protein
KeywordsTRANSFERASE / left-handed beta-helix / rossmann fold / acetyltransferase
Function / homology
Function and homology information


Bacterial sugar transferase / Bacterial sugar transferase / Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / 3 Solenoid ...Bacterial sugar transferase / Bacterial sugar transferase / Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylgalactosaminyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsMorrison, M.J. / Imperiali, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine.
Authors: Morrison, M.J. / Imperiali, B.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.6Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilin glycosylation protein


Theoretical massNumber of molelcules
Total (without water)21,0331
Polymers21,0331
Non-polymers00
Water1,964109
1
A: Pilin glycosylation protein

A: Pilin glycosylation protein

A: Pilin glycosylation protein


Theoretical massNumber of molelcules
Total (without water)63,0993
Polymers63,0993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4600 Å2
ΔGint-22 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.219, 86.219, 86.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

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Components

#1: Protein Pilin glycosylation protein


Mass: 21032.938 Da / Num. of mol.: 1 / Fragment: unp residues 197-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: NGO0085 / Plasmid: pET30b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS RIL / References: UniProt: Q5FAE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate pH 4.6, 20mM calcium chloride, 30% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionLimit h max: 29 / Limit h min: 0 / Limit k max: 51 / Limit k min: 1 / Limit l max: 51 / Limit l min: 0 / Number: 25105 / D res high: 1.669 Å / D res low: 38.558 Å / Num. obs: 25096
ReflectionResolution: 1.67→38.56 Å / Num. all: 25133 / Num. obs: 25105 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.37 Å2
Reflection scaleGroup code: 1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.55 Å38.56 Å
Translation5.55 Å38.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BSW

3bsw


Resolution: 1.67→38.558 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.15 / σ(F): 1.36 / Phase error: 17.71 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 1278 5.09 %RANDOM
Rwork0.167 ---
obs0.1681 25104 99.77 %-
all-25133 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.69 Å2 / Biso mean: 22.3885 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: LAST / Resolution: 1.67→38.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 0 109 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061454
X-RAY DIFFRACTIONf_angle_d1.1331988
X-RAY DIFFRACTIONf_chiral_restr0.078250
X-RAY DIFFRACTIONf_plane_restr0.004263
X-RAY DIFFRACTIONf_dihedral_angle_d10.441500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6686-1.73540.23171280.1932629275799
1.7354-1.81440.20441460.180726032749100
1.8144-1.910.18581230.169926442767100
1.91-2.02970.21641410.160926342775100
2.0297-2.18640.16921580.154825982756100
2.1864-2.40640.20341570.160426432800100
2.4064-2.75450.18581250.169226622787100
2.7545-3.470.16211410.167126742815100
3.47-38.56860.19331590.16822739289899

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