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- PDB-3lwh: Crystal structure of Cren7-dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 3lwh
TitleCrystal structure of Cren7-dsDNA complex
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / beta-sheet / DNA-binding / Methylation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


chromosome / double-stranded DNA binding / cytoplasm
Similarity search - Function
Chromatin protein Cren7 / Double-stranded DNA-binding Cren7 / Cren7 superfamily / Chromatin protein Cren7 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, Z.F. / Gong, Y. / Guo, L. / Jiang, T. / Huang, L.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA
Authors: Zhang, Z.F. / Gong, Y. / Guo, L. / Jiang, T. / Huang, L.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Chromatin protein Cren7
B: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
C: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5293
Polymers11,5293
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.693, 52.354, 88.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chromatin protein Cren7


Mass: 6677.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: creN7, SSO6901 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) plysS / References: UniProt: Q97ZE3
#2: DNA chain DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Mass: 2425.629 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.8
Details: 30% PEG1500, pH 6.8, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 9660 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 44
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 8.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JTM

2jtm


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.771 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 452 4.8 %RANDOM
Rwork0.21634 ---
all0.21774 8918 --
obs0.21774 8918 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.672 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2---0.57 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms463 322 0 78 863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3862.4761192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.418558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0123.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9921592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.284152
X-RAY DIFFRACTIONr_chiral_restr0.0650.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02510
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.2313
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2506
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6371.5298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1742479
X-RAY DIFFRACTIONr_scbond_it1.5343696
X-RAY DIFFRACTIONr_scangle_it1.9284.5713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 39 -
Rwork0.274 634 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4061-0.14720.21535.55092.91988.4773-0.0939-0.03550.174-0.0038-0.0626-0.0504-0.5475-0.14410.1564-0.22480.0319-0.038-0.2369-0.0045-0.213916.5917.1454.189
26.8116-4.2619-1.0897.84294.426510.2294-0.2595-0.1539-0.00670.10940.11350.1572-0.1788-0.28560.146-0.32890.064-0.0017-0.30130.0093-0.244716.2745.7648.495
30.3448-1.1661-1.36367.36041.54748.1398-0.0618-0.1195-0.04180.6323-0.45560.3214-0.2944-0.53070.5173-0.10650.07010.0342-0.0334-0.0423-0.06159.0688.3718.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 12
2X-RAY DIFFRACTION1A15 - 29
3X-RAY DIFFRACTION2A36 - 43
4X-RAY DIFFRACTION2A47 - 53
5X-RAY DIFFRACTION3B101 - 108
6X-RAY DIFFRACTION3C109 - 116

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