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- PDB-1o62: Crystal structure of the apo form of a PLP-dependent enzyme -

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Basic information

Entry
Database: PDB / ID: 1o62
TitleCrystal structure of the apo form of a PLP-dependent enzyme
Componentsaminotransferase
Keywordsstructural genomics / unknown function
Function / homology
Function and homology information


UDP-N-acetylbacillosamine transaminase / UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity / polysaccharide biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
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 ...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
ACETATE ION / BETA-MERCAPTOETHANOL / Aminotransferase homolog
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStructural GenomiX
CitationJournal: 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.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 24, 2015Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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: aminotransferase
B: aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,27511
Polymers89,6292
Non-polymers6469
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-52 kcal/mol
Surface area28100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.189, 152.189, 77.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein aminotransferase


Mass: 44814.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: TM0572 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S5Y7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 285 K / Method: hanging drop vapor diffusion / pH: 7.5
Details: pH 7.5, hanging drop vapor diffusion, temperature 285K
Components of the solutions
IDConc.NameCrystal-IDSol-ID
19.6mg/ml protein11
2150mM NaCl12
320mM Hepes12
410mM Methionine12
51mM beta-mercaptoethanol12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 58421 / Num. obs: 58421 / % possible obs: 98.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.3 / % possible all: 98.3
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.82 Å / σ(F): 0
RfactorNum. reflection
Rfree0.255 5950
Rwork0.224 -
obs-58421
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 228.826 Å2 / ksol: 0.898 e/Å3
Displacement parametersBiso mean: 27.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.569 Å2-0.284 Å20 Å2
2---0.569 Å20 Å2
3---0.853 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.1→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 36 412 6308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.413
X-RAY DIFFRACTIONp_planar_tor1.399
X-RAY DIFFRACTIONp_chiral_restr0.102
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_mcbond_it1.012
X-RAY DIFFRACTIONp_mcangle_it1.762
X-RAY DIFFRACTIONp_scbond_it1.694
X-RAY DIFFRACTIONp_scangle_it2.494
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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