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- PDB-1ne8: YDCE protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1ne8
TitleYDCE protein from Bacillus subtilis
Componentsconserved hypothetical protein YDCE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein YDCE / New York SGX Research Center for Structural Genomics / PSI / Protein Structure Initiative / NYSGXRC
Function / homology
Function and homology information


rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-1PG / ACETIC ACID / Endoribonuclease EndoA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsGogos, A. / Mu, H. / Bahna, F. / Gomez, C.A. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003
Title: Crystal structure of YdcE protein from Bacillus subtilis
Authors: Gogos, A. / Mu, H. / Bahna, F. / Gomez, C.A. / Shapiro, L.
History
DepositionDec 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein YDCE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6885
Polymers13,0631
Non-polymers6254
Water1,802100
1
A: conserved hypothetical protein YDCE
hetero molecules

A: conserved hypothetical protein YDCE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,37510
Polymers26,1262
Non-polymers1,2498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)56.630, 56.630, 138.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

21A-592-

HOH

DetailsThe second molecule of the putative biological dimer is generated by the following transformation: BIOMT1 0.5 -0.866 0.0 28.3175 BIOMT2 -0.866 -0.5 0.0 49.045 BIOMT3 0.0 0.0 -1.0 23.0431

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Components

#1: Protein conserved hypothetical protein YDCE


Mass: 13062.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ydcE / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P96622
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG 4,000 0.1M Sodium Acetate pH 4.6, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.9 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
45 mMdithiothreitol1drop
512 %PEG40001reservoir
60.1 Msodium acetate1reservoirpH4.6
70.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9790, 0.97938, 0.97163
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979381
30.971631
ReflectionResolution: 2.1→30 Å / Num. obs: 8231 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 19.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 8.86 / Num. unique all: 794 / Rsym value: 0.17 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 8244 / Num. measured all: 80833 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.198

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20.86 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 380 -random
Rwork0.1585 ---
all0.1619 8204 --
obs0.1619 8194 99.48 %-
Displacement parametersBiso mean: 22.098 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 27 108 1036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.019
X-RAY DIFFRACTIONr_angle_refined_deg1.6
X-RAY DIFFRACTIONr_chiral_restr0.12
LS refinement shellResolution: 2.1→2.155 Å /
RfactorNum. reflection
Rfree0.209 22
Rwork0.13 -
obs-547
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.64

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