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- PDB-3fle: SE_1780 protein of unknown function from Staphylococcus epidermidis. -

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Basic information

Entry
Database: PDB / ID: 3fle
TitleSE_1780 protein of unknown function from Staphylococcus epidermidis.
ComponentsSE_1780 protein
Keywordsstructural genomics / unknown function / APC61035.1 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Protein of unknown function DUF915, hydrolase-like / Alpha/beta hydrolase of unknown function (DUF915) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha/beta hydrolase / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.009 Å
AuthorsOsipiuk, J. / Hatzos, C. / Clancy, S. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of SE_1780 protein of unknown function from Staphylococcus epidermidis.
Authors: Osipiuk, J. / Hatzos, C. / Clancy, S. / Joachimiak, A.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SE_1780 protein
B: SE_1780 protein


Theoretical massNumber of molelcules
Total (without water)57,2882
Polymers57,2882
Non-polymers00
Water8,071448
1
A: SE_1780 protein


Theoretical massNumber of molelcules
Total (without water)28,6441
Polymers28,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SE_1780 protein


Theoretical massNumber of molelcules
Total (without water)28,6441
Polymers28,6441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.722, 41.458, 153.996
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121
Detailsa putative biological unit is a monomer based on PISA program

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Components

#1: Protein SE_1780 protein


Mass: 28644.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_1780 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CRJ5, UniProt: A0A0H2VHE3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 1000, 0.1 M Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.488
ReflectionResolution: 2.009→27 Å / Num. obs: 77366 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.114 / Χ2: 2.279 / Net I/σ(I): 15.682
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2 / Num. unique all: 1793 / Χ2: 0.967 / % possible all: 92.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.009→26.995 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.834 / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
Details: Refinement was performed using twin law -h,-k,l and twin fraction 0.49. Unknown ligands were modeled as waters in chains X and Y. THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflection
Rfree0.223 3810 5.33 %
Rwork0.181 --
all0.183 71468 -
obs0.183 71468 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.195 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 81.47 Å2 / Biso mean: 33.714 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.345 Å2-0 Å2-0.007 Å2
2---7.958 Å2-0 Å2
3---0.424 Å2
Refinement stepCycle: LAST / Resolution: 2.009→26.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 448 4344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083966
X-RAY DIFFRACTIONf_angle_d1.1125320
X-RAY DIFFRACTIONf_chiral_restr0.075560
X-RAY DIFFRACTIONf_plane_restr0.004692
X-RAY DIFFRACTIONf_dihedral_angle_d18.7421462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.009-2.0440.3141190.26825562675
2.044-2.0810.281600.26329773137
2.081-2.1210.2581770.26131443321
2.121-2.1640.3181730.25333033476
2.164-2.2110.3081740.24234743648
2.211-2.2630.3141600.24634283588
2.263-2.3190.281910.25135233714
2.319-2.3820.2592290.22834083637
2.382-2.4520.2781800.23135533733
2.452-2.5310.271800.22935473727
2.531-2.6220.2411740.21334653639
2.622-2.7270.2431950.20835253720
2.727-2.850.2432300.235323762
2.85-30.2422280.18635433771
3-3.1880.2141860.17535593745
3.188-3.4340.1741870.15734203607
3.434-3.7790.1611710.12634883659
3.779-4.3240.1441550.11134693624
4.324-5.440.1481450.11534153560
5.44-26.9980.2531990.19735263725

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