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- PDB-6d54: Low Temperature joint X-ray/neutron structure of DNA oligonucleot... -

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Basic information

Entry
Database: PDB / ID: 6d54
TitleLow Temperature joint 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 / 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: 1.65 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 19, 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 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)2,5693
Polymers2,5211
Non-polymers492
Water70339
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)5,1386
Polymers5,0412
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9340 Å2
ΔGint-16 kcal/mol
Surface area4680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.884, 41.884, 24.307
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
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
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORILL LADI III22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEDec 12, 2017osmic varimax
LADI III2IMAGE PLATENov 20, 2017collimators
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: 6D54

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.65-40286610010.40.056116.6
1.9-21.3162984.670.17929.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I) obs% possible all
1.65-1.7110.20.149116.6100
1.9-23.40.22625.366

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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: 61.45 Å2 / Biso mean: 24.54 Å2 / Biso min: 5.01 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: 92.2058 Å2 / ksol: 0.546925 e/Å3

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

4fp6

1.65-40X-RAY DIFFRACTION0.2460.231362843280098.2
1.9-21.3NEUTRON DIFFRACTION0.260.234651909157282.3
Refine analyze
Refine-ID#notag 0Luzzati coordinate error obs (Å)Luzzati d res low obs (Å)Luzzati sigma a obs (Å)Luzzati d res high obs
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.210.19
Luzzati d res low-5
Luzzati sigma a0.180.07
Luzzati d res high-1.65
NEUTRON DIFFRACTION0.2350.191.9
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms163 0 2 39 204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_torsion_deg0.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.95
NEUTRON DIFFRACTIONx_bond_d0.006
NEUTRON DIFFRACTIONx_angle_deg0.9
NEUTRON DIFFRACTIONx_torsion_deg0.7
NEUTRON DIFFRACTIONx_torsion_impr_deg0.95
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 (%)
1.65-1.730.511850.235317X-RAY DIFFRACTION0.1235533594.1
1.73-1.820.31185.60.219306X-RAY DIFFRACTION0.07333932495.6
1.82-1.930.268164.80.225315X-RAY DIFFRACTION0.06733833197.6
1.93-2.080.231113.30.228327X-RAY DIFFRACTION0.0734733897.4
2.08-2.290.211267.40.204326X-RAY DIFFRACTION0.04135735298.6
2.29-2.620.272113.20.222336X-RAY DIFFRACTION0.08234834799.4
2.62-3.30.174154.20.233345X-RAY DIFFRACTION0.04536136099.7
3.3-21.020.197215.30.244377X-RAY DIFFRACTION0.04340139899.3
1.9-1.990.27650.25149NEUTRON DIFFRACTION0.1123615565.7
1.99-2.090.24974.20.266161NEUTRON DIFFRACTION0.09422416874.7
2.09-2.220.201147.80.252166NEUTRON DIFFRACTION0.05423418076.6
2.22-2.390.25663.20.229179NEUTRON DIFFRACTION0.10422918580.8
2.39-2.630.24373.60.214186NEUTRON DIFFRACTION0.09223519382.1
2.63-3.010.18183.80.233204NEUTRON DIFFRACTION0.06424221287.6
3.01-3.790.2181880.207208NEUTRON DIFFRACTION0.05124322693
3.79-21.020.52683.20.252245NEUTRON DIFFRACTION0.18626925394.1

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