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- PDB-1t06: 1.9 A Crystal Structure of a Protein of Unknown Function from Bac... -

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Basic information

Entry
Database: PDB / ID: 1t06
Title1.9 A Crystal Structure of a Protein of Unknown Function from Bacillus cereus ATCC 14579
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Bacillus cereus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / DNA alkylation repair protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.9A crystal structure of a hypothetical protein from Bacillus cereus ATCC 14579
Authors: Zhang, R. / Wu, R. / Moy, S. / Joachimiak, A.
History
DepositionApr 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)53,0252
Polymers53,0252
Non-polymers00
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.959, 89.112, 121.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein may existed in dimmer, MolA and MolB present the dimmer in the asymmetric unit.

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Components

#1: Protein hypothetical protein


Mass: 26512.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81BA8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.35 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.2M NH4SO4, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 30, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 75781 / Num. obs: 72674 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.18
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.12 / Num. unique all: 7550 / % possible all: 77

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 359598.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3493 5 %RANDOM
Rwork0.196 ---
obs0.196 70510 92.7 %-
all-76062 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.222 Å2 / ksol: 0.305658 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--9.23 Å20 Å2
3----8.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 0 405 4119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 424 4.7 %
Rwork0.296 8587 -
obs--71.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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