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- PDB-1mdo: Crystal structure of ArnB aminotransferase with pyridomine 5' pho... -

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Basic information

Entry
Database: PDB / ID: 1mdo
TitleCrystal structure of ArnB aminotransferase with pyridomine 5' phosphate
ComponentsArnB 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.7 Å
AuthorsNoland, 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. ...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. / 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 1.3Dec 26, 2018Group: Data collection / Structure summary / Category: audit_author
Revision 1.4Nov 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: ArnB aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6902
Polymers43,4411
Non-polymers2481
Water8,593477
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ArnB aminotransferase
hetero molecules

A: ArnB aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3794
Polymers86,8832
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5480 Å2
ΔGint-40 kcal/mol
Surface area25080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.154, 91.154, 128.585
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 ArnB aminotransferase / putative DegT/DnrJ/EryC1/StrS family


Mass: 43441.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZNF3
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
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: 1.7→29.57 Å / Num. all: 60130 / Num. obs: 60130 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.79 Å / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 29.6 Å / % possible obs: 99.9 % / Redundancy: 13.7 % / Num. measured all: 827017 / Rmerge(I) obs: 0.127
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 1.609 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.57 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 2907 RANDOM
Rwork0.21 --
all0.2172 --
obs0.2172 60130 -
Refinement stepCycle: LAST / Resolution: 1.7→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 16 477 3206
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.217 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.78
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 5 Å / Num. reflection obs: 57454

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