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- PDB-5vbj: Sulfur as a bromine biomolecular halogen-bond acceptor -

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Basic information

Entry
Database: PDB / ID: 5vbj
TitleSulfur as a bromine biomolecular halogen-bond acceptor
ComponentsDNA (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3')
KeywordsDNA / Biophysics / Bromine / Sulfur / Halogen Bonding / Models / Molecular / Molecular Conformation / Uracil
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsFord, M.C. / Ho, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)5351441 United States
CitationJournal: J Phys Chem Lett / Year: 2017
Title: Sulfur as an Acceptor to Bromine in Biomolecular Halogen Bonds.
Authors: Ford, M.C. / Saxton, M. / Ho, P.S.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,2923
Polymers6,2522
Non-polymers401
Water50428
1
A: DNA (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5846
Polymers12,5044
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6580 Å2
ΔGint1 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.165, 23.981, 37.815
Angle α, β, γ (deg.)90.00, 112.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

21B-212-

HOH

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Components

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


Mass: 3125.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25 mM sodium cacodylate, 15 mM calcium chloride, 1.0 mM spermine, and 0.75 mM DNA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 3562 / % possible obs: 85.93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.944→34.982 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 563 9.9 %
Rwork0.2184 --
obs0.224 5686 74.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.944→34.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 28 433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009484
X-RAY DIFFRACTIONf_angle_d1.197735
X-RAY DIFFRACTIONf_dihedral_angle_d37.852174
X-RAY DIFFRACTIONf_chiral_restr0.05380
X-RAY DIFFRACTIONf_plane_restr0.00722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9443-2.140.4219710.4177697X-RAY DIFFRACTION40
2.14-2.44960.41421390.35421220X-RAY DIFFRACTION72
2.4496-3.08590.32271710.30041534X-RAY DIFFRACTION89
3.0859-34.98790.21971820.15531672X-RAY DIFFRACTION97

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