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- PDB-8tle: CDCA7 (Mouse) Binds Non-B-form 36-mer DNA oligo (sg C2-Form 1) -

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Basic information

Entry
Database: PDB / ID: 8tle
TitleCDCA7 (Mouse) Binds Non-B-form 36-mer DNA oligo (sg C2-Form 1)
Components
  • Cell division cycle-associated protein 7
  • ssDNA
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / zinc fingers / chromatin architecture / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of cell population proliferation / regulation of DNA-templated transcription / apoptotic process / nucleoplasm / nucleus / cytosol
Similarity search - Function
Zinc-finger domain of monoamine-oxidase A repressor R1 / CDCA7/CDA7L / Zinc-finger domain of monoamine-oxidase A repressor R1
Similarity search - Domain/homology
DNA / DNA (> 10) / Cell division cycle-associated protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsHorton, J.R. / Ren, R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Biorxiv / Year: 2023
Title: The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA.
Authors: Hardikar, S. / Ren, R. / Ying, Z. / Horton, J.R. / Bramble, M.D. / Liu, B. / Lu, Y. / Liu, B. / Dan, J. / Zhang, X. / Cheng, X. / Chen, T.
History
DepositionJul 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle-associated protein 7
X: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8178
Polymers27,5482
Non-polymers2696
Water21612
1
A: Cell division cycle-associated protein 7
X: ssDNA
hetero molecules

A: Cell division cycle-associated protein 7
X: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,63416
Polymers55,0964
Non-polymers53812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8140 Å2
ΔGint-70 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.666, 60.768, 49.090
Angle α, β, γ (deg.)90.000, 117.510, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11X-101-

MG

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Components

#1: Protein Cell division cycle-associated protein 7


Mass: 16452.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdca7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codon-plus (DE3)-RIL / References: UniProt: Q9D0M2
#2: DNA chain ssDNA


Mass: 11095.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: n vitro SELEX screening / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH8.5, 25%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→30.38 Å / Num. obs: 25246 / % possible obs: 97.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.047 / Net I/σ(I): 13.1
Reflection shellResolution: 2.08→2.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1147 / CC1/2: 0.919 / Rpim(I) all: 0.178 / % possible all: 85.6

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→30.38 Å / SU ML: 0.2726 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 1253 5.02 %
Rwork0.232 23705 -
obs0.2335 24958 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.9 Å2
Refinement stepCycle: LAST / Resolution: 2.08→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 470 6 12 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271367
X-RAY DIFFRACTIONf_angle_d0.50161946
X-RAY DIFFRACTIONf_chiral_restr0.0345211
X-RAY DIFFRACTIONf_plane_restr0.0051177
X-RAY DIFFRACTIONf_dihedral_angle_d21.5388556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.160.6361540.4864992X-RAY DIFFRACTION34.1
2.16-2.260.44511350.37952572X-RAY DIFFRACTION88.64
2.26-2.380.34721470.34982841X-RAY DIFFRACTION97.9
2.38-2.520.35711490.32132866X-RAY DIFFRACTION98.82
2.52-2.720.35051520.27932899X-RAY DIFFRACTION99.74
2.72-2.990.33351540.29692889X-RAY DIFFRACTION99.77
2.99-3.420.24661510.26022875X-RAY DIFFRACTION99.05
3.43-4.310.2351530.19862868X-RAY DIFFRACTION99.74
4.31-30.380.21141580.17122903X-RAY DIFFRACTION99.38
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)
10.09243082090790.058536184956-0.02315782585690.0021274109022-0.006876954551820.410872465689-0.506808248482-0.4292178332520.486752257259-0.5996816276810.6987219476920.5582858867590.2025188788990.577098560523-0.01454858244990.830423964326-0.05737889116320.07900770869010.8806726539030.04344409028470.418308542442-0.19378691159412.450714827812.1749164148
20.0460655379808-0.08825545228650.005900232116230.154299428984-0.06275695121090.0725166759441-0.2846979721980.7937805273470.709081779676-0.908679345-0.0696137742751-0.654642622528-0.234462385198-0.187405338497-0.0005972444126311.17698866747-0.1101133907550.5050585298621.014656579650.1393397022731.3403419724215.902609906113.36151610487.18002458789
30.660427553930.0440345088805-0.2947280348840.250406233887-0.3314533730850.982787930913-0.29670517532-0.2429016688240.0457235148682-0.348341994107-0.300317759993-1.30229567754-0.230951228397-0.0240921987898-0.04329473135130.530903631678-0.0161824052480.008086176214420.489918690220.03037564838980.95452708578610.974487173610.739235372221.6609723421
40.1651069944290.142845049524-0.2723646478860.6626633615650.3556129364020.988325895337-0.1120203184890.1770551026510.238979286824-0.407442235107-0.0567191022031-1.095094641140.218589297825-0.168509322375-0.009367476987560.5849780134210.008930516699250.2187548590780.5086886974370.08168336414870.7147587035598.067417576381.5944244347214.4414990733
50.6501461476870.756235181983-0.3045040953960.868770071633-0.3397400284740.148791163483-0.452322296011-1.04027095238-1.25494378019-0.250565038701-0.365159858788-0.26436658663-0.53468580975-0.507752291677-0.08951589462590.6335233396-0.0154340058655-0.1185162885270.693075865560.0447305665920.5267680947171.67944730754-4.4455221666625.2593328073
60.0007071270810350.005712090217480.03744298715330.02246877525870.0692767016580.09477939326660.02031944989450.5397425780870.0787913357105-0.2421560418020.1152812433330.5344083183640.514672619669-0.137128889664-8.75099434134E-50.741743580224-0.217912066466-0.2398915980350.85574001203-0.08441570656611.88994699016-48.136054638-2.9483313194812.8723706837
70.399761931223-0.656493771690.3684118403822.347552843320.224968757464-0.871865222862-0.0865275354335-0.0116053465597-0.4861782471010.008364962676530.25800984074-0.492531929761-0.0513752187589-0.1589949789510.2425878765480.549526582489-0.041042167738-0.03900196298570.715225368538-0.05156726956770.490252832765-5.339065955126.3476683227423.0204522497
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 244 through 252 )AA244 - 2521 - 9
22chain 'A' and (resid 253 through 262 )AA253 - 26210 - 19
33chain 'A' and (resid 263 through 297 )AA263 - 29720 - 54
44chain 'A' and (resid 298 through 335 )AA298 - 33555 - 92
55chain 'A' and (resid 336 through 346 )AA336 - 34693 - 103
66chain 'X' and (resid 8 through 12 )XB8 - 12
77chain 'X' and (resid 13 through 30 )XB13 - 30

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