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- PDB-6d4l: Joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2... -

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Basic information

Entry
Database: PDB / ID: 6d4l
TitleJoint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5
ComponentsDNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3')
KeywordsDNA / DNA oligonucleotide selenium modification
Function / homologyDEUTERATED WATER / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKovalevsky, A. / Huang, Z. / Vandavasi, V.G.
Citation
Journal: Structure / Year: 2018
Title: Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.
Authors: Vandavasi, V.G. / Blakeley, M.P. / Keen, D.A. / Hu, L.R. / Huang, Z. / Kovalevsky, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 2.0Mar 2, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / diffrn_source / entity / entity_poly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity_poly.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5452
Polymers2,5211
Non-polymers241
Water52229
1
A: DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0904
Polymers5,0412
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9080 Å2
ΔGint-28 kcal/mol
Surface area3250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.695, 42.695, 24.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3')


Mass: 2520.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M magnesium acetate, 30% MPD, 0.1 M MES

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORILL LADI III22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEJan 22, 2015osmic varimax
LADI III2IMAGE PLATEAug 15, 2015collimators
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
341
Reflection

Entry-ID: 6D4L

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.56-40341496.86.70.033145.8
2-20125774.25.60.17627.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I) obs% possible all
1.56-1.623.30.41712.176.8
2-2.112.80.28923.558.1

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
LAUEGENdata reduction
LSCALEdata scaling
CNSphasing
Refinement

Biso max: 90.31 Å2 / Biso mean: 27.66 Å2 / Biso min: 8.69 Å2 / % reflection Rfree: 5 % / R Free selection details: random / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: joint X_ray/neutron ML / Bsol: 300 Å2 / ksol: 0.642621 e/Å3

Starting modelResolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection obs (%)
PDB entry 4FP6

4fp6

1.56-40X-RAY DIFFRACTION0.2760.2421983484296084.6
2-20NEUTRON DIFFRACTION0.3120.25641717120470
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.20.2
Luzzati d res low-5
Luzzati sigma a-0.12
Luzzati d res high-1.56
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.50.31
Luzzati d res low-5
Luzzati sigma a0.510.56
Luzzati d res high-2
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.56→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms163 0 1 29 193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg0.5
X-RAY DIFFRACTIONx_torsion_impr_deg1.03
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg0.5
NEUTRON DIFFRACTIONx_torsion_impr_deg1.03
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.56-1.630.168950.298135X-RAY DIFFRACTION0.05642814433.6
1.63-1.720.198226.90.224295X-RAY DIFFRACTION0.04241631776
1.72-1.830.215236.40.225337X-RAY DIFFRACTION0.04541936085.9
1.83-1.970.2352360.231361X-RAY DIFFRACTION0.04942738489.9
1.97-2.170.309286.90.24376X-RAY DIFFRACTION0.05843640492.7
2.17-2.480.228256.10.248384X-RAY DIFFRACTION0.04643140994.9
2.48-3.120.262327.50.241395X-RAY DIFFRACTION0.04644542796
3.12-30.190.321316.60.245437X-RAY DIFFRACTION0.05848546896.3
2-2.090.434650.45296NEUTRON DIFFRACTION0.17721210248.1
2.09-2.20.242550.36496NEUTRON DIFFRACTION0.10820310149.5
2.2-2.340.53497.80.391106NEUTRON DIFFRACTION0.17820811555.3
2.34-2.520.455970.315120NEUTRON DIFFRACTION0.15221112961.1
2.52-2.770.231117.10.247144NEUTRON DIFFRACTION0.0720715574.9
2.77-3.170.352127.10.225158NEUTRON DIFFRACTION0.10221517079.1
3.17-3.990.209178.50.179183NEUTRON DIFFRACTION0.05121820091.7
3.99-19.090.33793.90.21223NEUTRON DIFFRACTION0.11224523294.7

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