[English] 日本語
Yorodumi
- PDB-4pta: Structure of MDR initiator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pta
TitleStructure of MDR initiator
ComponentsReplication initiator protein
KeywordsREPLICATION / initiation / multidrug resistance / PROTEIN BINDING
Function / homologyReplication initiator A, N-terminal / Replication initiator protein A, C-terminal domain / Replication initiator protein A (RepA) N-terminus / Replication initiator protein A C-terminal domain / Replication initiator protein / Replication initiator protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6003 Å
AuthorsSchumacher, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein.
Authors: Schumacher, M.A. / Tonthat, N.K. / Kwong, S.M. / Chinnam, N.B. / Liu, M.A. / Skurray, R.A. / Firth, N.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Replication initiator protein


Theoretical massNumber of molelcules
Total (without water)15,5191
Polymers15,5191
Non-polymers00
Water57632
1
D: Replication initiator protein

D: Replication initiator protein

D: Replication initiator protein

D: Replication initiator protein


Theoretical massNumber of molelcules
Total (without water)62,0754
Polymers62,0754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12830 Å2
ΔGint-45 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.460, 101.460, 62.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Replication initiator protein


Mass: 15518.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: USA300 / Gene: repA, SAUSA300_pUSA030001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FDD7, UniProt: A0A0H2XIV8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1 M Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 275K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012 / Details: mirrors
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→67 Å / Num. all: 5120 / Num. obs: 5166 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.332 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.6003→23.62 Å / SU ML: 0.39 / σ(F): 1.46 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 511 9.99 %
Rwork0.225 --
obs0.231 5116 97 %
all-5120 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.92 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5209 Å20 Å2-0 Å2
2--4.5209 Å20 Å2
3----9.0418 Å2
Refinement stepCycle: LAST / Resolution: 2.6003→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 0 32 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031038
X-RAY DIFFRACTIONf_angle_d0.6481402
X-RAY DIFFRACTIONf_dihedral_angle_d17.507396
X-RAY DIFFRACTIONf_chiral_restr0.042159
X-RAY DIFFRACTIONf_plane_restr0.002177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6003-2.86160.48081280.30621157X-RAY DIFFRACTION100
2.8616-3.27470.28631300.24561169X-RAY DIFFRACTION100
3.2747-4.12230.25491310.18911177X-RAY DIFFRACTION100
4.1223-23.62360.24841220.21911102X-RAY DIFFRACTION89

+
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