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- PDB-3bd1: Structure of the Cro protein from putative prophage element Xfaso... -

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Basic information

Entry
Database: PDB / ID: 3bd1
TitleStructure of the Cro protein from putative prophage element Xfaso 1 in Xylella fastidiosa strain Ann-1
ComponentsCro protein
KeywordsTRANSCRIPTION / transcription factor / helix-turn-helix / prophage / structural evolution
Function / homologylambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ACORN (Ddirect method) / Resolution: 1.4 Å
AuthorsHall, B.M. / Roberts, S.A. / Montfort, W.R. / Cordes, M.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds
Authors: Roessler, C.G. / Hall, B.M. / Anderson, W.J. / Ingram, W.M. / Roberts, S.A. / Montfort, W.R. / Cordes, M.H.
History
DepositionNov 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cro protein
B: Cro protein
C: Cro protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43110
Polymers24,8353
Non-polymers5967
Water2,774154
1
A: Cro protein
B: Cro protein
C: Cro protein
hetero molecules

A: Cro protein
B: Cro protein
C: Cro protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,86220
Polymers49,6706
Non-polymers1,19214
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_444-y-1,x-y-1,z-1/31
identity operation1_555x,y,z1
Buried area1020 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.970, 66.970, 54.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Cro protein


Mass: 8278.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: Ann-1 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3R0L1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, 1 mM TCEP-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2005
RadiationMonochromator: BENT Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.4→58.03 Å / Num. obs: 53726 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.61 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.048 / Χ2: 0.99 / Net I/σ(I): 13.3 / Scaling rejects: 1444
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.4-1.453.650.3863.21962753671.0199.7
1.45-1.513.650.3133.71962453670.9999.6
1.51-1.583.640.2484.5194705327199.8
1.58-1.663.650.1925.6197265385199.9
1.66-1.763.650.1387.51973453830.99100
1.76-1.93.680.1019.71969553210.9599.9
1.9-2.093.650.06314.81980253920.93100
2.09-2.393.640.04620.11969953760.93100
2.39-3.013.590.03526.81940153580.97100
3.01-17.063.250.02544.31571746701.1987.2

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDISPLAYFdata collection
d*TREKdata reduction
ACORNphasing
RefinementMethod to determine structure: ACORN (Ddirect method)
Starting model: PDB entry 2HIN

2hin


Resolution: 1.4→17.06 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.594 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2697 5.1 %RANDOM
Rwork0.147 ---
obs0.147 52945 98.5 %-
all-55642 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→17.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 35 154 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221518
X-RAY DIFFRACTIONr_bond_other_d0.0020.021072
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.972054
X-RAY DIFFRACTIONr_angle_other_deg2.732587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3545204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9221.56264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1051524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02317
X-RAY DIFFRACTIONr_nbd_refined0.2310.2357
X-RAY DIFFRACTIONr_nbd_other0.2370.21184
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2793
X-RAY DIFFRACTIONr_nbtor_other0.0820.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.28321261
X-RAY DIFFRACTIONr_mcbond_other3.9712399
X-RAY DIFFRACTIONr_mcangle_it5.57931565
X-RAY DIFFRACTIONr_scbond_it9.1769588
X-RAY DIFFRACTIONr_scangle_it12.14512482
X-RAY DIFFRACTIONr_rigid_bond_restr5.31233098
X-RAY DIFFRACTIONr_sphericity_free18.5883155
X-RAY DIFFRACTIONr_sphericity_bonded9.45432577
LS refinement shellResolution: 1.4→1.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 198 -
Rwork0.228 3798 -
all-3996 -
obs-3996 99.58 %

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