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- PDB-4q29: Ensemble Refinement of plu4264 protein from Photorhabdus luminescens -

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Basic information

Entry
Database: PDB / ID: 4q29
TitleEnsemble Refinement of plu4264 protein from Photorhabdus luminescens
Componentsplu4264 protein
KeywordsStructural Genomics / Unknown Function / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Midwest Center for Structural Genomics / MCSG / Cupin / PSI-Biology
Function / homology
Function and homology information


Polyketide biosynthesis protein CurC, predicted / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.349 Å
AuthorsWang, F. / Michalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Miller, M.D. / Thomas, M.G. ...Wang, F. / Michalska, K. / Li, H. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Weerth, S. / Miller, M.D. / Thomas, M.G. / Joachimiak, A. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2015
Title: Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 angstrom resolution.
Authors: Weerth, R.S. / Michalska, K. / Bingman, C.A. / Yennamalli, R.M. / Li, H. / Jedrzejczak, R. / Wang, F. / Babnigg, G. / Joachimiak, A. / Thomas, M.G. / Phillips, G.N.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: plu4264 protein
B: plu4264 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2765
Polymers31,1362
Non-polymers1403
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.738, 147.687, 83.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Number of models20
Components on special symmetry positions
IDModelComponents
18A-375-

HOH

29A-332-

HOH

312A-406-

HOH

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Components

#1: Protein plu4264 protein


Mass: 15567.780 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria)
Strain: TT01 / Gene: plu4264 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MZL9
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Li2SO4, 0.1 M Tris/HCl 8.5, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.349→30 Å / Num. all: 76260 / Num. obs: 76134 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.35→1.37 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.349→24.898 Å / SU ML: 0.07 / σ(F): 0.1 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1553 1111 1.46 %Same R-free flags with PDB entry 4MV2
Rwork0.1264 ---
all0.1268 76091 --
obs0.1268 75927 99.53 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso min: 99999 Å2
Refinement stepCycle: LAST / Resolution: 1.349→24.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 3 198 2229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_plane_restr0.011
X-RAY DIFFRACTIONf_chiral_restr0.121
X-RAY DIFFRACTIONf_dihedral_angle_d17.18
X-RAY DIFFRACTIONf_angle_d2.097
X-RAY DIFFRACTIONf_bond_d0.02
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3493-1.41070.23271250.18979233935899
1.4107-1.4850.19041550.159192559410100
1.485-1.5780.15111350.121992959430100
1.578-1.69990.12331230.10593039426100
1.6999-1.87090.13211430.099793219464100
1.8709-2.14150.14471270.106494049531100
2.1415-2.69750.14431540.108394049558100
2.6975-24.90190.16561490.14519601975099

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