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- PDB-1mdz: Crystal structure of ArnB aminotransferase with cycloserine and p... -

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Basic information

Entry
Database: PDB / ID: 1mdz
TitleCrystal structure of ArnB aminotransferase with cycloserine and pyridoxal 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 activity / 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
Chem-DCS / PYRIDOXAL-5'-PHOSPHATE / UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.07 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.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: Advisory / Data collection / Category: pdbx_database_remark / Item: _pdbx_database_remark.text
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 1.6Mar 26, 2025Group: 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 / 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
Remark 600HETEROGEN THE USE OF ALTERNATE CONFORMATION ID IN DCS AND PLP IN THIS ENTRY IS NOT TO INDICATE THAT ...HETEROGEN THE USE OF ALTERNATE CONFORMATION ID IN DCS AND PLP IN THIS ENTRY IS NOT TO INDICATE THAT THE ATOMS SPECIFIED HAVE MORE THAN ONE IDENTIFIABLE SITE. THERE IS ONLY ONE SITE FOR EACH ATOM IN DCS AND PLP, ALTHOUGH THE SITES HAVE PARTIAL OCCUPANCIES BECAUSE THE TWO LIGANDS ARE COMPETING FOR THE SAME SPACE.

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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)43,4123
Polymers42,8321
Non-polymers5802
Water4,576254
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)86,8246
Polymers85,6642
Non-polymers1,1614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6630 Å2
ΔGint-45 kcal/mol
Surface area24580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.904, 90.904, 127.710
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: 42831.785 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-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N3O7P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
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: 2.07→38.55 Å / Num. all: 33311 / Num. obs: 33311 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.07→2.18 Å / % possible all: 91.7
Reflection
*PLUS
Highest resolution: 2.08 Å / Lowest resolution: 38.6 Å / % possible obs: 99.4 % / Redundancy: 13.2 % / Num. measured all: 440660 / Rmerge(I) obs: 0.2
Reflection shell
*PLUS
% possible obs: 96.3 % / Redundancy: 8.6 % / Rmerge(I) obs: 1.419 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.07→38.55 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 1561 RANDOM
Rwork0.212 --
all0.2234 --
obs0.2234 33311 -
Refinement stepCycle: LAST / Resolution: 2.07→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 37 254 2998
Refinement
*PLUS
Highest resolution: 2.08 Å / Lowest resolution: 38.55 Å / Rfactor obs: 0.223 / Rfactor Rfree: 0.25
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_deg2.02
LS refinement shell
*PLUS
Highest resolution: 2.08 Å / Lowest resolution: 5 Å / Num. reflection obs: 30476

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