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- PDB-1mdx: Crystal structure of ArnB transferase with pyridoxal 5' phosphate -

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Basic information

Entry
Database: PDB / ID: 1mdx
TitleCrystal structure of ArnB transferase with pyridoxal 5' phosphate
ComponentsUDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
KeywordsTRANSFERASE / type 1 aminotransferase fold
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 / polysaccharide biosynthetic process / transaminase activity / lipid A biosynthetic process / pyridoxal phosphate binding / response to antibiotic / membrane
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
2-OXOGLUTARIC ACID / UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsNoland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T.A. / Rutter, M.E. / Sanderson, W.E. ...Noland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T.A. / Rutter, M.E. / Sanderson, W.E. / Muller-Dieckmann, H.-J. / Gajiwala, K.S. / Sauder, J.M. / Buchanan, S.G.
Citation
Journal: Structure / Year: 2002
Title: Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: A 4-amino-4-deoxy-L-arabinose lipopolysaccharide modifying enzyme
Authors: Noland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T. / Rutter, M.E. / Sanderson, W.E. / Muller-Dieckmann, H.-J. / Gajiwala, K. / Buchanan, S.G.
#1: Journal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.R.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry
Revision 1.4Oct 10, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.5Dec 26, 2018Group: Data collection / Structure summary / Category: audit_author / entity / Item: _entity.formula_weight
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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: UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3904
Polymers43,0601
Non-polymers3303
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)86,7808
Polymers86,1202
Non-polymers6616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8300 Å2
ΔGint-35 kcal/mol
Surface area24500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.152, 91.152, 128.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-402-

GOL

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Components

#1: Protein UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase / Polymyxin resistance protein PmrH / UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) ...Polymyxin resistance protein PmrH / UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) aminotransferase / UDP-Ara4O aminotransferase / UDP-4-amino-4-deoxy-L-arabinose aminotransferase


Mass: 43059.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: arnB, pbgP, pbgP1, pmrH, STM2297 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZNF3, UDP-4-amino-4-deoxy-L-arabinose aminotransferase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 60.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: sodium citrate, PEG 10000, beta-mercaptoethanol, pH 5.5, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
2100 mMsodium citrate1reservoirpH5.5
318-22 %PEG100001reservoir
41 mMbeta-mercaptoethanol1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.96→45.58 Å / Num. all: 39164 / Num. obs: 39164 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.96→2.07 Å / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 45.6 Å / Redundancy: 13.7 % / Num. measured all: 537578 / Rmerge(I) obs: 0.153
Reflection shell
*PLUS
% possible obs: 94.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.96→45.58 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1833 RANDOM
Rwork0.198 --
all0.2064 --
obs0.2064 39164 -
Refinement stepCycle: LAST / Resolution: 1.96→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 37 442 3229
Refinement
*PLUS
Lowest resolution: 45.58 Å / % reflection Rfree: 5 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.76
LS refinement shell
*PLUS
Highest resolution: 1.96 Å / Lowest resolution: 5 Å / Num. reflection obs: 36413

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