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- PDB-4f1r: Structure analysis of the global metabolic regulator Crc from Pse... -

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Basic information

Entry
Database: PDB / ID: 4f1r
TitleStructure analysis of the global metabolic regulator Crc from Pseudomonas aeruginos
ComponentsCatabolite repression control protein
KeywordsTRANSCRIPTION REGULATOR / Catabolite Repression Control / post-transcription regulator
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: 2.201 Å
AuthorsZhang, H. / Wei, Y. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Iubmb Life / Year: 2013
Title: Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.
Authors: Wei, Y. / Zhang, H. / Gao, Z.Q. / Xu, J.H. / Liu, Q.S. / Dong, Y.H.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / 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
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

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Assembly

Deposited unit
A: Catabolite repression control protein


Theoretical massNumber of molelcules
Total (without water)33,6151
Polymers33,6151
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.299, 74.299, 123.575
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: 33614.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: crc / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q51380
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.9M succinic acid pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 20524 / Num. obs: 20524 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 54.82
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1006 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WG8

1wg8


Resolution: 2.201→34.692 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1035 5.11 %RANDOM
Rwork0.2022 ---
all0.2044 20524 --
obs0.2044 20273 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.285 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6664 Å2-0 Å2-0 Å2
2--15.6664 Å20 Å2
3----31.3328 Å2
Refinement stepCycle: LAST / Resolution: 2.201→34.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 0 23 2130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072169
X-RAY DIFFRACTIONf_angle_d1.0362937
X-RAY DIFFRACTIONf_dihedral_angle_d16.606805
X-RAY DIFFRACTIONf_chiral_restr0.078299
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2011-2.31710.36551370.3254266396
2.3171-2.46220.37791670.2949266699
2.4622-2.65230.28671480.2507274199
2.6523-2.91910.31121430.2502273699
2.9191-3.34120.27281450.21762771100
3.3412-4.20830.22911520.18592815100
4.2083-34.69620.2071430.1713284696
Refinement TLS params.Method: refined / Origin x: -31.1686 Å / Origin y: 17.9614 Å / Origin z: 10.9351 Å
111213212223313233
T0.5384 Å2-0.0771 Å20.0288 Å2-0.4394 Å2-0.0022 Å2--0.4417 Å2
L1.8907 °20.1063 °2-0.5073 °2-2.1051 °2-0.4492 °2--3.9929 °2
S0.0063 Å °0.009 Å °0.0541 Å °-0.0502 Å °0.0729 Å °-0.0116 Å °-0.3324 Å °0.0076 Å °-0.0653 Å °
Refinement TLS groupSelection details: ALL

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