[English] 日本語
Yorodumi
- PDB-4hte: Crystal Structure of the C-terminal domain of Nicking Enzyme from... -

+
Open data


ID or keywords:

Loading...

-
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
MobA/MobL family protein
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicking enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2142
Polymers42,1741
Non-polymers401
Water00
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: MAD

-
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))

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more