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- PDB-4ppm: Crystal structure of PigE: a transaminase involved in the biosynt... -

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Basic information

Entry
Database: PDB / ID: 4ppm
TitleCrystal structure of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14
ComponentsAminotransferase
KeywordsTRANSFERASE / transaminase
Function / homology
Function and homology information


pyridoxal binding / Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / : / Aminotransferase PigE
Similarity search - Component
Biological speciesSerratia sp. FS14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLou, X.D. / Ran, T.T. / Xu, D.Q. / Wang, W.W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of the catalytic domain of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14
Authors: Lou, X.D. / Ran, T.T. / Han, N. / Gao, Y. / He, J. / Tang, L. / Xu, D.Q. / Wang, W.W.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,4036
Polymers188,8602
Non-polymers5434
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-99 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.100, 228.100, 67.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Aminotransferase / PigE


Mass: 94429.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. FS14 (bacteria) / Strain: FS14 / Gene: L085_23050 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059ZJX2, UniProt: A0A0J9X1Q5*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.4M, 0.49M Sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic, 50mM MgCl2, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 88591 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
BALBESphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.89 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.207 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.206 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27181 4443 5 %RANDOM
Rwork0.23781 ---
obs0.23952 84144 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.16 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7117 0 32 344 7493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197242
X-RAY DIFFRACTIONr_bond_other_d0.0010.026986
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9729807
X-RAY DIFFRACTIONr_angle_other_deg0.947316020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7365916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46123.639316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.696151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2461552
X-RAY DIFFRACTIONr_chiral_restr0.1140.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021666
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5433.7053676
X-RAY DIFFRACTIONr_mcbond_other3.5333.7043675
X-RAY DIFFRACTIONr_mcangle_it5.1095.5414588
X-RAY DIFFRACTIONr_mcangle_other5.1095.5424589
X-RAY DIFFRACTIONr_scbond_it4.1154.2073566
X-RAY DIFFRACTIONr_scbond_other4.1144.2063567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2326.1325220
X-RAY DIFFRACTIONr_long_range_B_refined8.28230.4518522
X-RAY DIFFRACTIONr_long_range_B_other8.25430.428457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 318 -
Rwork0.346 6162 -
obs--99.6 %

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