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- PDB-3kxt: Crystal structure of Sulfolobus Cren7-dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 3kxt
TitleCrystal structure of Sulfolobus Cren7-dsDNA complex
Components
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
  • Chromatin protein Cren7
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / CRENARCHAEA CHROMATIN PROTEIN / MINOR-GROOVE BINDING / METHYLATION / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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: 1.602 Å
AuthorsFeng, Y. / Wang, J.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex
Authors: Feng, Y. / Yao, H. / Wang, J.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,1733
Polymers11,1733
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-11 kcal/mol
Surface area5710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.190, 53.115, 90.753
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: 6317.527 Da / Num. of mol.: 1 / Fragment: residues 6-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO6901 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE3
#2: DNA chain 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0mM complex, 0.1M tri-sodium citrate dihydrate pH 5.6, 20% (v/v) iso-propanol, 20% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→18.06 Å / Num. obs: 16134 / % possible obs: 97.2 % / Redundancy: 9.6 % / Rsym value: 0.077 / Net I/σ(I): 37.262
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.35 / % possible all: 83.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES; 2JTM, 1AZP

2jtm

1azp


Resolution: 1.602→16.732 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.846 / SU ML: 0.14 / σ(F): 0.02 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 765 5.09 %
Rwork0.1759 14277 -
obs0.178 15042 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.385 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso max: 123.87 Å2 / Biso mean: 41.316 Å2 / Biso min: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1--5.455 Å20 Å2-0 Å2
2--7.355 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.602→16.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms445 322 0 135 902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01818
X-RAY DIFFRACTIONf_angle_d1.6131168
X-RAY DIFFRACTIONf_chiral_restr0.073126
X-RAY DIFFRACTIONf_plane_restr0.00793
X-RAY DIFFRACTIONf_dihedral_angle_d24.35334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6018-1.72530.23981140.20242421X-RAY DIFFRACTION79
1.7253-1.89870.22341420.18962777X-RAY DIFFRACTION88
1.8987-2.1730.2311580.18193027X-RAY DIFFRACTION97
2.173-2.73580.22811800.18323030X-RAY DIFFRACTION97
2.7358-16.73340.20441710.16563022X-RAY DIFFRACTION92
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)
15.60560.42091.10415.59982.41161.2261-0.166-1.06260.2790.23590.3047-0.0982-0.20860.0172-0.1310.2958-0.01320.00370.4204-0.05260.23947.674718.751722.4542
27.59695.71635.4946.18717.46339.8402-0.4417-0.89540.9169-0.12680.30720.5279-1.36670.59570.03960.3557-0.0438-0.01170.2237-0.10940.28795.895924.943620.4358
31.85660.02370.49070.33760.12231.0666-0.0489-0.187-0.20210.21090.0474-0.06680.30320.1608-0.020.27550.0686-0.00210.21050.00520.23719.915610.874713.6388
42.0066-0.71170.6682.31870.75152.3982-0.2075-0.0070.0657-0.1704-0.0023-0.0973-0.3041-0.15440.18540.26630.0789-0.01520.2599-0.01550.20224.420920.254114.0456
54.6489-1.26970.08421.7777-1.44794.4328-0.1452-0.8916-0.02840.05760.0824-0.37790.57680.88340.21580.39570.1639-0.04860.52460.06810.303212.97739.235722.2502
63.4306-1.2323-0.42714.97951.65020.5894-0.15470.4093-0.4591-0.48670.0885-0.34150.4020.2750.10030.3230.06640.04760.3224-0.02990.274715.52917.36672.8963
74.7953-1.7537-0.07561.02860.89981.9244-0.03710.3506-0.38950.0225-0.1390.35530.0275-0.19110.14310.28150.0178-0.0340.2407-0.01920.24250.717912.2026.1358
82.93730.99472.25662.43873.05054.1938-0.01381.2401-0.0484-0.49630.118-0.3576-0.71710.8446-0.11110.3699-0.0043-0.0630.4792-0.02840.27325.532615.2645-0.9116
97.0734-3.1032-3.76462.20013.18815.2609-0.2178-0.47140.7545-0.07590.4185-0.3416-0.0260.9249-0.24460.25680.03870.03650.3761-0.0260.281618.502315.03938.7419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:12)A5 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:21)A13 - 21
3X-RAY DIFFRACTION3(chain A and resid 22:44)A22 - 44
4X-RAY DIFFRACTION4(chain A and resid 45:54)A45 - 54
5X-RAY DIFFRACTION5(chain A and resid 55:60)A55 - 60
6X-RAY DIFFRACTION6(chain B and resid 101:104)B101 - 104
7X-RAY DIFFRACTION7(chain B and resid 105:108)B105 - 108
8X-RAY DIFFRACTION8(chain C and resid 109:112)C109 - 112
9X-RAY DIFFRACTION9(chain C and resid 113:116)C113 - 116

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