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- PDB-4ht4: Molecular Basis of Vancomycin Resistance Transfer in Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 4ht4
TitleMolecular Basis of Vancomycin Resistance Transfer in Staphylococcus aureus
Components
  • DNA (28-MER)
  • Nicking enzyme
KeywordsHydrolase/DNA / vancomycin resistance plasmid / DNA relaxase / S. aureus / conjugative transfer / DNA hairpin / Hydrolase-DNA complex
Function / homology
Function and homology information


MobA/MobL protein / MobA/MobL family / BirA Bifunctional Protein; domain 2 - #30 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DNA / DNA (> 10) / Nicking enzyme
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.907 Å
AuthorsEdwards, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus.
Authors: Edwards, J.S. / Betts, L. / Frazier, M.L. / Pollet, R.M. / Kwong, S.M. / Walton, W.G. / Ballentine, W.K. / Huang, J.J. / Habibi, S. / Del Campo, M. / Meier, J.L. / Dervan, P.B. / Firth, N. / Redinbo, M.R.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.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_ref_seq_dif.details / _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: Nicking enzyme
B: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,12512
Polymers31,7102
Non-polymers41510
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-96 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.226, 63.226, 313.756
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein Nicking enzyme


Mass: 23069.264 Da / Num. of mol.: 1 / Mutation: F25Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nes, NES from pLW1043 / Plasmid: pCPD-lasso / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: Q53632
#2: DNA chain DNA (28-MER)


Mass: 8640.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oriT DNA hairpin

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Non-polymers , 4 types, 29 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8,000, 120 mM calcium acetate, 80 mM sodium cacolydate, and 20% glycerol v/v , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH ANOMALOUS / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 20.3 % / Av σ(I) over netI: 47.95 / Number: 179546 / Rmerge(I) obs: 0.097 / Χ2: 2.15 / D res high: 2.9 Å / D res low: 100 Å / Num. obs: 8865 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.871009610.0676.45317.5
6.257.8799.210.0754.81520.3
5.466.2510010.0783.45521.1
4.965.4699.110.0793.00821.4
4.64.9699.610.0762.52921.8
4.334.610010.0772.20321.4
4.114.3399.310.0831.97222.1
3.944.1199.810.0841.87122.6
3.783.9499.410.1031.72622.1
3.653.7899.310.1271.66823
3.543.6599.510.1331.42422.9
3.443.5499.610.1371.24822.8
3.353.4499.510.1571.20323
3.273.3599.810.1791.13622.8
3.193.2799.510.2291.05921.5
3.123.1999.510.2141.02918.1
3.063.1299.610.2561.01316.4
33.0695.910.2111.04314.9
2.95388.110.261.02713.7
2.92.9579.710.2611.0213.2
ReflectionResolution: 2.9→100 Å / Num. obs: 8865 / % possible obs: 97.7 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.097 / Χ2: 2.15 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.9513.20.2613451.02179.7
2.95-313.70.263851.027188.1
3-3.0614.90.2113971.043195.9
3.06-3.1216.40.2564461.013199.6
3.12-3.1918.10.2144341.029199.5
3.19-3.2721.50.2294241.059199.5
3.27-3.3522.80.1794431.136199.8
3.35-3.44230.1574291.203199.5
3.44-3.5422.80.1374461.248199.6
3.54-3.6522.90.1334381.424199.5
3.65-3.78230.1274361.668199.3
3.78-3.9422.10.1034591.726199.4
3.94-4.1122.60.0844281.871199.8
4.11-4.3322.10.0834451.972199.3
4.33-4.621.40.0774642.2031100
4.6-4.9621.80.0764602.529199.6
4.96-5.4621.40.0794623.008199.1
5.46-6.2521.10.0784773.4551100
6.25-7.8720.30.0755004.815199.2
7.87-10017.50.0675476.453196

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.907→48.509 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7129 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 412 4.7 %
Rwork0.2294 8351 -
obs0.2322 8763 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.36 Å2 / Biso mean: 75.774 Å2 / Biso min: 27.62 Å2
Refinement stepCycle: LAST / Resolution: 2.907→48.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 577 10 19 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032244
X-RAY DIFFRACTIONf_angle_d0.7383157
X-RAY DIFFRACTIONf_chiral_restr0.05333
X-RAY DIFFRACTIONf_plane_restr0.002318
X-RAY DIFFRACTIONf_dihedral_angle_d22.969860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9074-3.3280.39471290.27432567269693
3.328-4.19260.33361280.23182768289699
4.1926-48.5160.24291550.216730163171100

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