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- PDB-1u61: Crystal Structure of Putative Ribonuclease III from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 1u61
TitleCrystal Structure of Putative Ribonuclease III from Bacillus cereus
Componentshypothetical protein
Keywordsstructural genomics / unknown function / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / rRNA processing / rRNA binding / cytoplasm
Similarity search - Function
Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of conserved hypothetical protein from Bacillus cereus
Authors: Osipiuk, J. / Quartey, P. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)15,6781
Polymers15,6781
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.978, 168.978, 168.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-210-

HOH

31A-211-

HOH

41A-212-

HOH

Detailsthe biological assembly is unknown

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Components

#1: Protein hypothetical protein


Mass: 15678.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC0111 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81J58
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 6.5 Å3/Da / Density % sol: 80.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 12, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 22651 / Num. obs: 22642 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 82 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 76
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 43.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1560 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 2.128 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1894 -RANDOM
Rwork0.20374 ---
all0.20729 22604 --
obs0.20729 22604 99.88 %-
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: 22.129 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 77 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211043
X-RAY DIFFRACTIONr_bond_other_d0.0020.02953
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9461410
X-RAY DIFFRACTIONr_angle_other_deg0.87332204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6565126
X-RAY DIFFRACTIONr_chiral_restr0.0910.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021162
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02219
X-RAY DIFFRACTIONr_nbd_refined0.2540.2242
X-RAY DIFFRACTIONr_nbd_other0.2420.21043
X-RAY DIFFRACTIONr_nbtor_other0.090.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3830.25
X-RAY DIFFRACTIONr_mcbond_it0.9311.5630
X-RAY DIFFRACTIONr_mcangle_it1.80221009
X-RAY DIFFRACTIONr_scbond_it2.9963413
X-RAY DIFFRACTIONr_scangle_it4.9594.5401
LS refinement shellResolution: 2.15→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.203 120
Rwork0.206 1637
obs-1637
Refinement TLS params.Method: refined / Origin x: 25.9393 Å / Origin y: 33.0257 Å / Origin z: -5.4684 Å
111213212223313233
T0.0153 Å20.0451 Å20.0127 Å2-0.1762 Å2-0.0268 Å2--0.1042 Å2
L0.7696 °2-0.3072 °2-0.4514 °2-0.9135 °20.0052 °2--0.7969 °2
S0.0727 Å °0.1352 Å °0.0177 Å °-0.0592 Å °-0.0776 Å °0.0231 Å °0.0663 Å °0.0835 Å °0.0049 Å °

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