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- PDB-4hte: Crystal Structure of the C-terminal domain of Nicking Enzyme from... -

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Basic information

Entry
Database: PDB / ID: 4hte
TitleCrystal Structure of the C-terminal domain of Nicking Enzyme from Staphylococcus aureus
ComponentsNicking enzyme
KeywordsHYDROLASE / vancomycin resistance plasmid / DNA relaxase / conjugative transfer / NES Cterminal domain / alpha-helical
Function / homology
Function and homology information


Regulator of G-protein Signalling 4; domain 2 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1730 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1740 / MobA/MobL protein / MobA/MobL family / Regulator of G-protein Signalling 4; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsBetts, L.
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
DepositionNov 1, 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: Refinement description / Category: 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicking enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2142
Polymers42,1741
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.284, 75.284, 179.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Nicking enzyme / / OriT nickase / OriT nickase Nes / OriT relaxase Nes


Mass: 42173.566 Da / Num. of mol.: 1 / Fragment: unp residues 254-593 / Mutation: E404A, K4045, E406A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: nes, NES from pLW1043, PGO1_p08, SAP014A_018, SAP015D_002, SAP068A_007, SAP069A_033, SAP079A_020, SAP080A_038, SAP082A_025, VRA0057
Plasmid: pCPD-lasso / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: O87361
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12-16% PEG 6000, 0.1 M Tris-HCl pH 8.0, 0.5 M LiCl, 12.5% glycerol, and 5% PEG-400, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97935,0.97954, 0.94936
DetectorDetector: CCD / Date: Aug 1, 2011
RadiationProtocol: MULTIPLE WAVELENGTH ANOMALOUS SCATTERING / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979541
30.949361
ReflectionResolution: 3→100 Å / Num. obs: 11051 / % possible obs: 99.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3-3.059.70.772.81100
3.05-3.119.70.5954.061100
3.11-3.179.60.5274.061100
3.17-3.239.70.4664.91100
3.23-3.39.60.3641100
3.3-3.389.60.2841100
3.38-3.469.60.2171100
3.46-3.569.60.1991100
3.56-3.669.70.1511100
3.66-3.789.50.1341100
3.78-3.919.50.1071100
3.91-4.079.60.0891100
4.07-4.269.50.0821100
4.26-4.489.40.0721100
4.48-4.769.40.0661100
4.76-5.139.30.0671100
5.13-5.659.30.0671100
5.65-6.469.10.0641100
6.46-8.148.90.05199.3
8.14-1008.10.03670195.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 3→45.809 Å / Occupancy max: 1 / Occupancy min: 0.56 / SU ML: 0.41 / σ(F): 0.79 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 1097 10.01 %
Rwork0.2674 --
obs0.2699 10958 99.76 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.338 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8312 Å2-0 Å20 Å2
2---1.8312 Å2-0 Å2
3---3.6623 Å2
Refinement stepCycle: LAST / Resolution: 3→45.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 1 0 2676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032717
X-RAY DIFFRACTIONf_angle_d0.5533688
X-RAY DIFFRACTIONf_dihedral_angle_d15.263977
X-RAY DIFFRACTIONf_chiral_restr0.036410
X-RAY DIFFRACTIONf_plane_restr0.001491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.13660.43021340.36841210X-RAY DIFFRACTION100
3.1366-3.30190.40641320.33271188X-RAY DIFFRACTION100
3.3019-3.50870.30931350.29751205X-RAY DIFFRACTION100
3.5087-3.77950.31051350.27211223X-RAY DIFFRACTION100
3.7795-4.15960.24561350.24181210X-RAY DIFFRACTION100
4.1596-4.7610.23581370.22171239X-RAY DIFFRACTION100
4.761-5.99620.31811390.28921251X-RAY DIFFRACTION100
5.9962-45.81420.25471500.23731335X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14660.95260.05622.4054-0.6511.60340.0754-1.07590.23040.5547-0.15680.13080.4763-0.14020.15411.3643-0.13890.23090.19810.0440.444952.57159.8758169.6853
22.7167-1.6422-0.85242.83240.89512.60230.0827-0.2619-0.10460.4867-0.01310.0339-0.24940.93930.02040.8126-0.06110.10990.2347-0.01250.359868.340330.3374163.4201
35.21171.191.87312.61520.9184.66480.0806-0.13060.1881-0.00430.1747-0.309-0.90390.3779-0.13830.5526-0.09620.13160.68730.0030.385880.907126.1326137.802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 254:389))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 395:514))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 516:593))

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