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

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Basic information

Entry
Database: PDB / ID: 3lis
TitleCrystal Structure of the Restriction-Modification Controller Protein C.Csp231I (Monoclinic form)
ComponentsCsp231I C protein
KeywordsTRANSCRIPTION / transcriptional regulator / helix-turn-helix / DNA binding protein / restriction modification control
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 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csp231I C protein
B: Csp231I C protein


Theoretical massNumber of molelcules
Total (without water)22,7602
Polymers22,7602
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-24 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.010, 29.530, 64.380
Angle α, β, γ (deg.)90.000, 101.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 96 / Label seq-ID: 1 - 96

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Csp231I C protein


Mass: 11380.236 Da / Num. of mol.: 2
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.: 88 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M malate-MES-Tris (MMT), 20% PEG 1500, pH 7.0, 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: Apr 7, 2009
RadiationMonochromator: Double crystal / 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. obs: 12439 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.057 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1821 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.96 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å18.7 Å
Translation2.5 Å18.7 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→31.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.843 / SU R Cruickshank DPI: 0.24 / SU Rfree: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 648 5.2 %RANDOM
Rwork0.207 ---
obs0.209 11784 99.05 %-
all-12432 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.97 Å2 / Biso mean: 33.417 Å2 / Biso min: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å21.15 Å2
2--1.42 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 0 88 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221590
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9822130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1175190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23423.33378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1761518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211174
X-RAY DIFFRACTIONr_mcbond_it4.41.5956
X-RAY DIFFRACTIONr_mcangle_it5.59921530
X-RAY DIFFRACTIONr_scbond_it6.2513634
X-RAY DIFFRACTIONr_scangle_it8.194.5600
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 784 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.10.05
TIGHT THERMAL1.480.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 48 -
Rwork0.24 858 -
all-906 -
obs--99.78 %

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