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- PDB-5ff5: Crystal Structure of SeMet PaaA -

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Basic information

Entry
Database: PDB / ID: 5ff5
TitleCrystal Structure of SeMet PaaA
ComponentsPaaA
KeywordsTRANSFERASE / Adenylyltransferase
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine dehydratase / cyclic threonylcarbamoyladenosine biosynthetic process / ubiquitin-like modifier activating enzyme activity
Similarity search - Function
: / PaaA-like, N-terminal domain / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PaaA
Similarity search - Component
Biological speciesEnterobacter agglomerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.933 Å
AuthorsBiernat, K.B. / Redinbo, M.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A.
Authors: Ghodge, S.V. / Biernat, K.A. / Bassett, S.J. / Redinbo, M.R. / Bowers, A.A.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: 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_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PaaA
B: PaaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,05510
Polymers86,3362
Non-polymers7198
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-117 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.962, 170.409, 64.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PaaA


Mass: 43168.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter agglomerans (bacteria) / Gene: paaA / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q9ZAR3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, magnesium sulfate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.93→29.48 Å / Num. obs: 16878 / % possible obs: 99.7 % / Redundancy: 25.3 % / Biso Wilson estimate: 66.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.024 / Net I/σ(I): 24.9 / Num. measured all: 427046 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.93-3.1125.10.6046.96645126510.970.12399.4
8.79-29.4821.50.05957.8149646970.9990.01297.4

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.933→29.475 Å / FOM work R set: 0.7379 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.289 1667 9.98 %
Rwork0.2098 15040 -
obs0.2178 16707 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.93 Å2 / Biso mean: 57.48 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.933→29.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 63 12 4738
Biso mean--77.21 52.94 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094794
X-RAY DIFFRACTIONf_angle_d1.3016500
X-RAY DIFFRACTIONf_chiral_restr0.055748
X-RAY DIFFRACTIONf_plane_restr0.006846
X-RAY DIFFRACTIONf_dihedral_angle_d14.4431677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9326-3.01880.36781260.25911189131596
3.0188-3.11610.34171360.2261210134697
3.1161-3.22730.33561310.21591214134598
3.2273-3.35640.30691380.2071231136999
3.3564-3.50890.31691380.20651232137099
3.5089-3.69360.30131340.19491241137599
3.6936-3.92450.26261410.19331258139999
3.9245-4.22670.26451300.192312771407100
4.2267-4.65060.27781450.18112571402100
4.6506-5.32010.27291440.205712721416100
5.3201-6.68980.28241430.245412901433100
6.6898-29.47680.28621610.222113691530100

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