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- PDB-4ri1: Crystal structure of Helicobacter pylori pseudaminic acid biosynt... -

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Basic information

Entry
Database: PDB / ID: 4ri1
TitleCrystal structure of Helicobacter pylori pseudaminic acid biosynthesis N -acetyltransferase PseH complex with acetyl-coA
ComponentsUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
KeywordsTRANSFERASE / GNAT family / N-acetyl transferase / acetyl-CoA / none
Function / homology
Function and homology information


UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETATE ION / UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å
AuthorsRoujeinikova, A. / Ud-Din, A.I.
CitationJournal: Plos One / Year: 2015
Title: Crystal Structure of Helicobacter pylori Pseudaminic Acid Biosynthesis N-Acetyltransferase PseH: Implications for Substrate Specificity and Catalysis.
Authors: Ud-Din, A.I. / Liu, Y.C. / Roujeinikova, A.
History
DepositionOct 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
B: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
C: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6529
Polymers66,0463
Non-polymers2,6066
Water4,107228
1
A: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
hetero molecules

A: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7686
Polymers44,0312
Non-polymers1,7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area4740 Å2
ΔGint-15 kcal/mol
Surface area17660 Å2
MethodPISA
2
B: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
C: UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7686
Polymers44,0312
Non-polymers1,7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-15 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.830, 145.620, 166.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11C-1453-

HOH

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Components

#1: Protein UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase / Pseudaminic acid biosynthesis protein H


Mass: 22015.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0327, HP_0327, pseH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: O25094, UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 4.94 Å3/Da / Density % sol: 75.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.2
Details: 0.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2, 3 mM acetyl-CoA, VAPOR DIFFUSION, HANGING DROP, temperature 2930.9 M diammonium tartrate, 80 mM sodium acetate trihydrate ...Details: 0.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2, 3 mM acetyl-CoA, VAPOR DIFFUSION, HANGING DROP, temperature 2930.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2 and acetyl-CoA at a concentration of 3 mMK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 54332 / % possible obs: 93.8 % / Observed criterion σ(F): 168694 / Observed criterion σ(I): 168694

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.3→29.989 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 2746 5.06 %5% omitted at random
Rwork0.1776 ---
obs0.1796 54302 93.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 165 228 4873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084787
X-RAY DIFFRACTIONf_angle_d1.0516454
X-RAY DIFFRACTIONf_dihedral_angle_d15.0821735
X-RAY DIFFRACTIONf_chiral_restr0.044653
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.37731330.28522617X-RAY DIFFRACTION96
2.3397-2.38220.34241390.27472604X-RAY DIFFRACTION96
2.3822-2.4280.30321330.25742626X-RAY DIFFRACTION95
2.428-2.47750.31281520.25692592X-RAY DIFFRACTION95
2.4775-2.53140.29991360.24362599X-RAY DIFFRACTION95
2.5314-2.59020.26011580.2222589X-RAY DIFFRACTION95
2.5902-2.6550.2611420.22292600X-RAY DIFFRACTION95
2.655-2.72670.25831410.2142613X-RAY DIFFRACTION95
2.7267-2.80690.26631230.20912594X-RAY DIFFRACTION94
2.8069-2.89740.23861200.20892597X-RAY DIFFRACTION94
2.8974-3.00090.26161350.20612634X-RAY DIFFRACTION94
3.0009-3.12090.21931460.1832542X-RAY DIFFRACTION94
3.1209-3.26280.23221280.1762600X-RAY DIFFRACTION93
3.2628-3.43460.21881480.18142555X-RAY DIFFRACTION93
3.4346-3.64940.2261400.17112539X-RAY DIFFRACTION92
3.6494-3.93060.19411390.15832562X-RAY DIFFRACTION92
3.9306-4.32510.1811310.13692549X-RAY DIFFRACTION91
4.3251-4.94860.15151430.12482537X-RAY DIFFRACTION91
4.9486-6.22550.19361290.14942466X-RAY DIFFRACTION87
6.2255-29.99110.16831300.15452541X-RAY DIFFRACTION86

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