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- PDB-4jg3: Crystal structure of catabolite repression control protein (crc) ... -

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Basic information

Entry
Database: PDB / ID: 4jg3
TitleCrystal structure of catabolite repression control protein (crc) from Pseudomonas aeruginosa
ComponentsCatabolite repression control protein
KeywordsUNKNOWN FUNCTION / AP endonuclease protein family
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Catabolite repression control protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrishkovskaya, I. / Milojevic, T. / Sonnleitner, E. / Blaesi, U. / Djinovic-Carugo, K.
CitationJournal: Plos One / Year: 2013
Title: The Pseudomonas aeruginosa Catabolite Repression Control Protein Crc Is Devoid of RNA Binding Activity
Authors: Milojevic, T. / Grishkovskaya, I. / Sonnleitner, E. / Djinovic-Carugo, K. / Blasi, U.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Catabolite repression control protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1372
Polymers30,1021
Non-polymers351
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.659, 74.659, 123.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Catabolite repression control protein


Mass: 30101.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: crc / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)(pLysS / References: UniProt: Q51380
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%(w/v) PEG1500, 40mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→44.59 Å / Num. all: 37275 / Num. obs: 37261 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2073 / % possible all: 95.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2jc5

2jc5


Resolution: 1.8→44.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.801 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1856 5 %RANDOM
Rwork0.19397 ---
obs0.19529 35360 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.784 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å21.39 Å20 Å2
2--1.39 Å20 Å2
3----4.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 1 125 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022059
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9463012
X-RAY DIFFRACTIONr_angle_other_deg1.00134720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78323.443122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391522
X-RAY DIFFRACTIONr_chiral_restr0.1460.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 122 -
Rwork0.328 2506 -
obs--95.42 %

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