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- PDB-6ssd: Transaminase with PLP bound -

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Basic information

Entry
Database: PDB / ID: 6ssd
TitleTransaminase with PLP bound
ComponentsForI-PLP
KeywordsTRANSFERASE / PLP bound
Function / homologyAspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 3-Layer(aba) Sandwich / Alpha Beta / PYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesStreptomyces kaniharaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ForI-PLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8983
Polymers44,5551
Non-polymers3432
Water11,908661
1
A: ForI-PLP
hetero molecules

A: ForI-PLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7976
Polymers89,1102
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10400 Å2
ΔGint-80 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.300, 92.300, 118.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ForI-PLP


Mass: 44555.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.95 Å3/Da / Density % sol: 58.33 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.18→72.89 Å / Num. obs: 156410 / % possible obs: 93.2 % / Redundancy: 23.6 % / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 22.3
Reflection shellResolution: 1.18→1.2 Å / Num. unique obs: 4974 / CC1/2: 0.5 / Rrim(I) all: 1.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→43.02 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.779 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1286 7817 5 %RANDOM
Rwork0.1111 ---
obs0.112 148310 93.11 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.19 Å2 / Biso mean: 17.774 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.18→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 5 661 3808
Biso mean--31.39 32.44 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193501
X-RAY DIFFRACTIONr_bond_other_d0.0020.023258
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9714822
X-RAY DIFFRACTIONr_angle_other_deg1.01337595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23923.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92915570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5141527
X-RAY DIFFRACTIONr_chiral_restr0.1140.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214080
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02726
X-RAY DIFFRACTIONr_rigid_bond_restr1.86536759
X-RAY DIFFRACTIONr_sphericity_free22.2665432
X-RAY DIFFRACTIONr_sphericity_bonded6.99356876
LS refinement shellResolution: 1.18→1.211 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 380 -
Rwork0.256 7167 -
all-7547 -
obs--61.65 %

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