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- PDB-3qxr: Crystal structure of the brominated CKIT-1 proto-oncogene promote... -

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Basic information

Entry
Database: PDB / ID: 3qxr
TitleCrystal structure of the brominated CKIT-1 proto-oncogene promoter quadruplex DNA
Components5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'
KeywordsDNA / DNA quadruplex / regulation / ckit-1
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsWei, D. / Parkinson, G.N. / Neidle, S.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.
Authors: Wei, D. / Parkinson, G.N. / Reszka, A.P. / Neidle, S.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Jun 6, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'
B: 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,58713
Polymers14,1872
Non-polymers40011
Water3,801211
1
A: 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3378
Polymers7,0931
Non-polymers2447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2505
Polymers7,0931
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.570, 51.350, 58.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-26-

K

21A-72-

HOH

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Components

#1: DNA chain 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*(BRU)P*GP*GP*GP*AP*GP*GP*AP*GP*GP*G)-3'


Mass: 7093.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, potassium chloride, sodium chloride, sodium cacodylate, potassium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.62→38.55 Å / Num. all: 14007 / Num. obs: 14007 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.5
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 61.8

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Processing

Software
NameVersionClassificationNB
DNAdata collection
PHASESphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1K8P

1k8p


Resolution: 1.62→26.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.172 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUAL DENSITY AROUND ATOM OP2 OF RESIDUES A19 AND G20 OF CHAIN B WAS NOT IDENTIFIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21325 700 5 %RANDOM
Rwork0.16608 ---
obs0.16849 13279 93.12 %-
all-14007 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.143 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.62→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 938 11 211 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.97631676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02513
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.68731084
X-RAY DIFFRACTIONr_scangle_it3.7314.51676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.616→1.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 39 -
Rwork0.236 627 -
obs--61.21 %

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