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- PDB-3on1: The structure of a protein with unknown function from Bacillus ha... -

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Basic information

Entry
Database: PDB / ID: 3on1
TitleThe structure of a protein with unknown function from Bacillus halodurans C
ComponentsBH2414 protein
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyRibosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta / BH2414 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsFan, Y. / Kagan, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a protein with unknown function from Bacillus halodurans C
Authors: Fan, Y. / Kagan, O. / Savchenko, A. / Joachimiak, A. / Edwards, A.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH2414 protein


Theoretical massNumber of molelcules
Total (without water)11,0331
Polymers11,0331
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.239, 51.141, 55.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH2414 protein


Mass: 11032.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2414 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KA76
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Na formate 4M, 221NDSB 0.3M, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 4, 2010 / Details: mirror
RadiationMonochromator: Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 11377 / Num. obs: 11377 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 58.76
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 11.34 / Num. unique all: 465 / % possible all: 81.6

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→37.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.442 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20271 547 4.8 %RANDOM
Rwork0.18356 ---
all0.18449 10740 --
obs0.18449 10740 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 0 107 858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022893
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9791215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18923.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15215185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.25159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02670
X-RAY DIFFRACTIONr_mcbond_it0.6281.5568
X-RAY DIFFRACTIONr_mcangle_it1.1822924
X-RAY DIFFRACTIONr_scbond_it1.8923325
X-RAY DIFFRACTIONr_scangle_it3.2044.5291
X-RAY DIFFRACTIONr_rigid_bond_restr0.7883893
LS refinement shellResolution: 1.655→1.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 49 -
Rwork0.234 753 -
obs--94.35 %

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