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- PDB-5w9s: Zinc finger of human CXXC5 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 5w9s
TitleZinc finger of human CXXC5 in complex with CpG DNA
Components
  • CXXC-type zinc finger protein 5
  • CpG DNA fragment
KeywordsDNA BINDING PROTEIN/DNA / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


methyl-CpG binding / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / Estrogen-dependent gene expression / sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
CXXC-type zinc finger protein CXXC4/CXXC5 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / CXXC-type zinc finger protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 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: CpG DNA fragment
B: CpG DNA fragment
C: CXXC-type zinc finger protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8897
Polymers15,6633
Non-polymers2274
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-23 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 40.110, 81.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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DNA chain / Protein , 2 types, 3 molecules ABC

#1: DNA chain CpG DNA fragment


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Protein CXXC-type zinc finger protein 5 / CF5 / Putative MAPK-activating protein PM08 / Putative NF-kappa-B-activating protein 102 / Retinoid- ...CF5 / Putative MAPK-activating protein PM08 / Putative NF-kappa-B-activating protein 102 / Retinoid-inducible nuclear factor / RINF


Mass: 8335.792 Da / Num. of mol.: 1 / Fragment: Zinc finger domain (UNP residues 254-306)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXXC5, HSPC195, TCCCIA00297 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q7LFL8

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Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 30% PEG-5000-MME, 0.2M ammonium sulfate, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→34.74 Å / Num. obs: 8535 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Net I/σ(I): 34.9 / Num. measured all: 96584
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1611.11.0132.678337070.7740.3151.061100
8.91-34.7410.30.021112119611610.0070.02299.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data reduction
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4hp3

4hp3


Resolution: 2.1→34.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.434 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.176
Details: The amino acid sequence of the search model was adjusted with Chainsaw after molecular replacement. Coot was used for interactive model re-building. molprobity and the parvati server were ...Details: The amino acid sequence of the search model was adjusted with Chainsaw after molecular replacement. Coot was used for interactive model re-building. molprobity and the parvati server were used for the analysis of model geometry and anisotropic ADPs, respectively.
RfactorNum. reflection% reflection
Rfree0.2537 396 4.7 %
Rwork0.2185 --
obs0.2202 8107 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.14 Å2 / Biso mean: 49.286 Å2 / Biso min: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å2-0 Å2
2---0.95 Å2-0 Å2
3---3.09 Å2
Refinement stepCycle: final / Resolution: 2.1→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms333 486 8 12 839
Biso mean--62.09 38.5 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.014914
X-RAY DIFFRACTIONr_bond_other_d0.0040.02613
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.4471329
X-RAY DIFFRACTIONr_angle_other_deg1.5823.0111411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.429543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86618.57114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0541569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.237157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02211
X-RAY DIFFRACTIONr_mcbond_it1.8552.803175
X-RAY DIFFRACTIONr_mcbond_other1.8522.794174
X-RAY DIFFRACTIONr_mcangle_it2.5524.186217
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 32 -
Rwork0.302 590 -
all-622 -
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)
17.4198-2.8345-1.31131.36271.55944.4056-0.25-0.5845-0.39670.13940.14890.14230.18810.04370.10110.0342-0.004-0.020.34260.08520.08552.075911.1902-5.2935
28.6819-0.6472-1.4610.97111.47942.3189-0.0767-0.0435-0.40550.02480.0210.03920.0820.0110.05580.0640.00380.00510.34260.07520.07252.013810.5076-6.8468
34.08440.4359-0.94294.5395-2.45177.61960.3947-0.06-0.0646-0.5755-0.26180.7356-0.0996-0.1158-0.13290.14190.0567-0.120.179-0.03830.13422.883216.7178-17.129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C258 - 301

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