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- PDB-4oca: Cryatal structure of ArnB K188A complexted with PLP and UDP-Ara4N -

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Basic information

Entry
Database: PDB / ID: 4oca
TitleCryatal structure of ArnB K188A complexted with PLP and UDP-Ara4N
ComponentsUDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
KeywordsTRANSFERASE / Aminotransferase
Function / homology
Function and homology information


UDP-4-amino-4-deoxy-L-arabinose aminotransferase / UDP-4-amino-4-deoxy-L-arabinose aminotransferase / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic
Similarity search - Function
UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2QR / UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase / UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSousa, M.C. / Lee, M.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Basis for Substrate Specificity in ArnB. A Key Enzyme in the Polymyxin Resistance Pathway of Gram-Negative Bacteria.
Authors: Lee, M. / Sousa, M.C.
History
DepositionJan 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5672
Polymers41,8011
Non-polymers7661
Water2,360131
1
A: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
hetero molecules

A: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1344
Polymers83,6012
Non-polymers1,5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4560 Å2
ΔGint-36 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.952, 90.952, 129.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase / UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) aminotransferase / UDP-4-amino-4-deoxy-L- ...UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) aminotransferase / UDP-4-amino-4-deoxy-L-arabinose aminotransferase


Mass: 41800.684 Da / Num. of mol.: 1 / Mutation: K188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: yfbE, arnB / Production host: Escherichia coli (E. coli)
References: UniProt: F5ZUF5, UniProt: A0A3Z6NYY1*PLUS, UDP-4-amino-4-deoxy-L-arabinose aminotransferase
#2: Chemical ChemComp-2QR / (2R,3R,4S,5S)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]tetrahydro-2H-pyr an-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / PLP-UDP-Ara4N


Mass: 766.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33N4O20P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium Citrate (pH4.5), 19 % PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorDate: Jan 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→37.18 Å / Num. obs: 29611
Reflection shellResolution: 2.3→2.4 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.179 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1160 4.98 %
Rwork0.2264 --
obs0.2281 23304 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 49 131 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032885
X-RAY DIFFRACTIONf_angle_d0.6923939
X-RAY DIFFRACTIONf_dihedral_angle_d12.651032
X-RAY DIFFRACTIONf_chiral_restr0.028451
X-RAY DIFFRACTIONf_plane_restr0.003501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.3251490.26992794X-RAY DIFFRACTION97
2.4047-2.53150.41661490.32642731X-RAY DIFFRACTION95
2.5315-2.690.2681520.28282863X-RAY DIFFRACTION99
2.69-2.89760.31291600.27492865X-RAY DIFFRACTION99
2.8976-3.18910.27831510.25152910X-RAY DIFFRACTION100
3.1891-3.65020.33381370.25632672X-RAY DIFFRACTION91
3.6502-4.59750.18281100.17412179X-RAY DIFFRACTION73
4.5975-37.18350.19321520.17443130X-RAY DIFFRACTION99

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