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- PDB-2ohw: Crystal structure of the YueI protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2ohw
TitleCrystal structure of the YueI protein from Bacillus subtilis
ComponentsYueI protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyProtein of unknown function DUF1694 / Protein of unknown function (DUF1694) / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YueI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsBonanno, J.B. / Jin, X. / Mu, H. / Dickey, M. / Bain, K.T. / Wu, B. / Chen, T. / Reyes, C. / Wasserman, S. / Smith, D. ...Bonanno, J.B. / Jin, X. / Mu, H. / Dickey, M. / Bain, K.T. / Wu, B. / Chen, T. / Reyes, C. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the YueI protein from Bacillus subtilis
Authors: Bonanno, J.B. / Jin, X. / Mu, H. / Dickey, M. / Bain, K.T. / Wu, B. / Chen, T. / Reyes, C. / Wasserman, S. / Smith, D. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Dec 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: YueI protein
B: YueI protein


Theoretical massNumber of molelcules
Total (without water)30,5592
Polymers30,5592
Non-polymers00
Water2,180121
1
A: YueI protein


Theoretical massNumber of molelcules
Total (without water)15,2791
Polymers15,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YueI protein


Theoretical massNumber of molelcules
Total (without water)15,2791
Polymers15,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.895, 39.443, 48.778
Angle α, β, γ (deg.)89.880, 108.050, 110.260
Int Tables number1
Space group name H-MP1
Detailsprobable monomer

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Components

#1: Protein YueI protein


Mass: 15279.444 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yueI / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32092
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Tris-HCl pH 7.5, 28% PEG 1000, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2006
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.4→46.08 Å / Num. all: 42599 / Num. obs: 42599 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.7 / Num. measured all: 15478 / Num. unique all: 5711 / Rsym value: 0.577 / % possible all: 86.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.358 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2135 5 %RANDOM
Rwork0.202 ---
obs0.204 42531 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.65 Å20.48 Å2
2--0.17 Å20.55 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 0 121 2201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222127
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9792877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49824.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53215390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7071514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021600
X-RAY DIFFRACTIONr_nbd_refined0.210.2850
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.224
X-RAY DIFFRACTIONr_mcbond_it0.9331.51316
X-RAY DIFFRACTIONr_mcangle_it1.46922068
X-RAY DIFFRACTIONr_scbond_it2.4423914
X-RAY DIFFRACTIONr_scangle_it3.6614.5808
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 140 -
Rwork0.265 2556 -
obs-2696 81.97 %

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