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- PDB-3lfp: Crystal Structure of the Restriction-Modification Controller Prot... -

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Basic information

Entry
Database: PDB / ID: 3lfp
TitleCrystal Structure of the Restriction-Modification Controller Protein C.Csp231I
ComponentsCsp231I C protein
KeywordsTRANSCRIPTION / transcriptional regulator / DNA binding protein / helix-turn-helix / restriction-modification
Function / homology
Function and homology information


Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCitrobacter sp. RFL231 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMcGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Analysis of a Novel Class of R-M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231.
Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Taylor, J.E. / Shevtsov, M.B. / Kneale, G.G.
History
DepositionJan 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
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: Csp231I C protein


Theoretical massNumber of molelcules
Total (without water)11,3801
Polymers11,3801
Non-polymers00
Water1,15364
1
A: Csp231I C protein

A: Csp231I C protein


Theoretical massNumber of molelcules
Total (without water)22,7602
Polymers22,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation70_445z-1/4,-y-1/4,x+1/41
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.370, 137.370, 137.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

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Components

#1: Protein Csp231I C protein


Mass: 11380.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RFL231 (bacteria) / Gene: csp231IC / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q32WH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2009
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7979 / Num. obs: 7753 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 38.7 % / Biso Wilson estimate: 35.293 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 42.78
Reflection shellResolution: 2→2.1 Å / Redundancy: 38.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 11.3 / Num. measured obs: 42928 / Num. unique all: 991 / Num. unique obs: 1052 / % possible all: 94.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
GDAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1Y7Y

1y7y


Resolution: 2→19.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.871 / SU B: 2.794 / SU ML: 0.083 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 365 4.6 %RANDOM
Rwork0.176 ---
obs0.178 7566 99.92 %-
all-7931 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.25 Å2 / Biso mean: 41.169 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: LAST / Resolution: 2→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 0 64 848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022795
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9821065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.941595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39423.33339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97815161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.519159
X-RAY DIFFRACTIONr_chiral_restr0.140.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021587
X-RAY DIFFRACTIONr_mcbond_it1.2681.5478
X-RAY DIFFRACTIONr_mcangle_it2.292765
X-RAY DIFFRACTIONr_scbond_it3.5953317
X-RAY DIFFRACTIONr_scangle_it5.9244.5300
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 29 -
Rwork0.161 534 -
all-563 -
obs-534 100 %

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