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- PDB-3esi: Crystal structure of an uncharacterized protein from Erwinia caro... -

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Basic information

Entry
Database: PDB / ID: 3esi
TitleCrystal structure of an uncharacterized protein from Erwinia carotovora subsp. atroseptica. Northeast Structural Genomics target EwR179
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / protein from Erwinia carotovora subsp. atroseptica (Pectobacterium atrosepticum) / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology: / Dehydrase, ECs4332, predicted / ApeI dehydratase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / ApeI dehydratase-like domain-containing protein
Function and homology information
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from Erwinia carotovora subsp. atroseptica. Northeast Structural Genomics target EwR179
Authors: Seetharaman, J. / Lew, S. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)58,6074
Polymers58,6074
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-18 kcal/mol
Surface area12490 Å2
Unit cell
Length a, b, c (Å)71.141, 71.141, 146.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
uncharacterized protein


Mass: 14651.850 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: ECA4500 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CYK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 293 K / pH: 5.6
Details: peg4k, 200mM NH4Acetate, 100mM Na3citrate ph5.6, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X4C20.979
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 49294 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.046 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 14 / Num. unique all: 4932 / Rsym value: 0.196 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→35.05 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 171847.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2366 5 %RANDOM
Rwork0.244 ---
obs0.244 47621 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9999 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å20 Å2
2---4.35 Å20 Å2
3---8.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 0 74 4030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 324 4.4 %
Rwork0.309 7022 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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