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- PDB-6sse: Transaminase with PMP bound -

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Basic information

Entry
Database: PDB / ID: 6sse
TitleTransaminase with PMP bound
ComponentsForI-PMP
KeywordsTRANSFERASE / PMP bound
Function / homologyAspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 3-Layer(aba) Sandwich / Alpha Beta / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesStreptomyces kaniharaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNaismith, J.H. / Gao, S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.
Authors: Gao, S. / Liu, H. / de Crecy-Lagard, V. / Zhu, W. / Richards, N.G.J. / Naismith, J.H.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ForI-PMP
B: ForI-PMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0879
Polymers89,1102
Non-polymers9777
Water16,340907
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-124 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.264, 125.828, 142.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 425
2010B2 - 425

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Components

#1: Protein ForI-PMP


Mass: 44555.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Li2SO4, 100 mM Tris-HCl pH 8.0 and 30 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→94.39 Å / Num. obs: 148308 / % possible obs: 98.8 % / Redundancy: 9.7 % / CC1/2: 1 / Net I/σ(I): 8
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 6922 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→94.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.674 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 7367 5 %RANDOM
Rwork0.1674 ---
obs0.1687 140719 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.72 Å2 / Biso mean: 19.726 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.56→94.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 57 907 7218
Biso mean--33.25 32.69 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176155
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6339138
X-RAY DIFFRACTIONr_angle_other_deg1.5761.56914237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06121.242322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.189151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1211550
X-RAY DIFFRACTIONr_chiral_restr0.1070.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021423
Refine LS restraints NCS

Ens-ID: 1 / Number: 13778 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.56→1.599 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.297 514 -
Rwork0.286 9851 -
obs--94.61 %

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