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- PDB-4uoy: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate -

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Basic information

Entry
Database: PDB / ID: 4uoy
TitleCrystal structure of YgjG in complex with Pyridoxal-5'-phosphate
ComponentsPUTRESCINE AMINOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Putrescine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Putrescine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
FORMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Putrescine aminotransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: Plos One / Year: 2014
Title: Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases.
Authors: Cha, H.J. / Jeong, J. / Rojviriya, C. / Kim, Y.
History
DepositionJun 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PUTRESCINE AMINOTRANSFERASE
B: PUTRESCINE AMINOTRANSFERASE
C: PUTRESCINE AMINOTRANSFERASE
D: PUTRESCINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,36011
Polymers203,1414
Non-polymers1,2197
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31250 Å2
ΔGint-215.2 kcal/mol
Surface area52440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.945, 129.319, 131.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PUTRESCINE AMINOTRANSFERASE / PUTRESCINE--2-OXOGLUTARIC ACID TRANSAMINASE / PAT / PATASE / PUTRESCINE--2-OXOGLUTARIC ACID ...PUTRESCINE--2-OXOGLUTARIC ACID TRANSAMINASE / PAT / PATASE / PUTRESCINE--2-OXOGLUTARIC ACID TRANSAMINASE / YGJG


Mass: 50785.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN K 300 AND PYRIDOXAL-5'-PHOSPHATE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B84(DE3)
References: UniProt: P42588, putrescine-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY ATTACHED TO THE K 300 OF EACH CHAINS.

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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: 2.58 Å3/Da / Density % sol: 52.44 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5 15% PEG 3350 0.2 M SODIUM FORMATE 0.1 MM N-DODECYL-N,N-DIMETHYLGLYCINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 91029 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 23.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VEF

1vef


Resolution: 2.305→29.746 Å / SU ML: 0.34 / σ(F): 1.49 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1990 2.2 %
Rwork0.1806 --
obs0.1818 89419 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→29.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13731 0 76 351 14158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914063
X-RAY DIFFRACTIONf_angle_d1.13619027
X-RAY DIFFRACTIONf_dihedral_angle_d15.2285172
X-RAY DIFFRACTIONf_chiral_restr0.0412162
X-RAY DIFFRACTIONf_plane_restr0.0052486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3048-2.36240.331330.26915841X-RAY DIFFRACTION93
2.3624-2.42630.3111340.2476090X-RAY DIFFRACTION97
2.4263-2.49760.29151490.23376101X-RAY DIFFRACTION97
2.4976-2.57820.2731380.22476127X-RAY DIFFRACTION97
2.5782-2.67030.32451390.21826181X-RAY DIFFRACTION98
2.6703-2.77710.28031510.20926198X-RAY DIFFRACTION98
2.7771-2.90340.25181310.19716243X-RAY DIFFRACTION98
2.9034-3.05630.2451440.19166240X-RAY DIFFRACTION98
3.0563-3.24760.25451480.19236271X-RAY DIFFRACTION99
3.2476-3.4980.22651470.18256322X-RAY DIFFRACTION99
3.498-3.84940.20711440.16076370X-RAY DIFFRACTION100
3.8494-4.40480.2141450.14046365X-RAY DIFFRACTION99
4.4048-5.54380.16881340.13886418X-RAY DIFFRACTION99
5.5438-29.74860.16951530.14466662X-RAY DIFFRACTION100

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