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- PDB-1r7l: 2.0 A Crystal Structure of a Phage Protein from Bacillus cereus A... -

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Basic information

Entry
Database: PDB / ID: 1r7l
Title2.0 A Crystal Structure of a Phage Protein from Bacillus cereus ATCC 14579
ComponentsPhage proteinBacteriophage
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / phage protein / two layers alpha-beta sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyBacillus phage protein / Bacillus phage protein-like / Bacillus phage protein-like / Phage ABA sandwich domain / Phage ABA sandwich domain / 2-Layer Sandwich / Alpha Beta / Phage protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, G. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2006
Title: Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold
Authors: Zhang, R. / Joachimiak, G. / Jiang, S. / Cipriani, A. / Collart, F. / Joachimiak, A.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage protein
B: Phage protein


Theoretical massNumber of molelcules
Total (without water)24,9972
Polymers24,9972
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.002, 66.338, 53.966
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMolecule A and molecule B represent the dimer in the asymmetric unit.

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Components

#1: Protein Phage protein / Bacteriophage


Mass: 12498.479 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: Q81EU2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 8000, 0.1M MES, 0.2M Ca(OAc)2, pH 6.0, 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, 0.9798, 0.9465
DetectorType: SBC-2 / Detector: CCD / Date: Oct 20, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.94651
ReflectionResolution: 2→50 Å / Num. all: 17716 / Num. obs: 17557 / % possible obs: 99.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 8.12 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.25 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 444377.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1628 5 %RANDOM
Rwork0.223 ---
obs0.223 32415 93.8 %-
all-34558 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.0238 Å2 / ksol: 0.378568 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.14 Å20 Å2-2.27 Å2
2---3.42 Å20 Å2
3----4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 0 102 1792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 256 5.4 %
Rwork0.314 4497 -
obs--82.7 %
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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