[English] 日本語
Yorodumi
- PDB-4lqe: Crystal Structure of MepB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lqe
TitleCrystal Structure of MepB
ComponentsMepB
KeywordsDNA BINDING PROTEIN / Endonuclease
Function / homologyMepB-like / MepB-like / MepB-like superfamily / MepB-like / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Multidrug transporter / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFaham, S. / Agah, S.
CitationJournal: Protein Sci. / Year: 2014
Title: Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases.
Authors: Agah, S. / Poulos, S. / Banchs, C. / Faham, S.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3552
Polymers19,2591
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MepB
hetero molecules

A: MepB
hetero molecules

A: MepB
hetero molecules

A: MepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4208
Polymers77,0364
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10090 Å2
ΔGint-126 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.645, 91.139, 100.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein MepB


Mass: 19258.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: MepB, SAV0335 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q99WP1, UniProt: A0A0H3JPI4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Bis-tris, pH 5.0, 2.3 M NH4SO4, 1% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 12092 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5 / Num. unique all: 969 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
CRANKphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→23.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27938 595 4.9 %RANDOM
Rwork0.23587 ---
obs0.23804 11449 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.861 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å20 Å2
2--5.77 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 5 74 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221258
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9521705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9252562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89215210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.596153
X-RAY DIFFRACTIONr_chiral_restr0.0960.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021957
X-RAY DIFFRACTIONr_mcbond_it0.6581.5746
X-RAY DIFFRACTIONr_mcangle_it1.22121198
X-RAY DIFFRACTIONr_scbond_it1.8753512
X-RAY DIFFRACTIONr_scangle_it2.6484.5506
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 45 -
Rwork0.345 799 -
obs--95.05 %
Refinement TLS params.Method: refined / Origin x: 12.719 Å / Origin y: 13.763 Å / Origin z: 66.023 Å
111213212223313233
T0.1025 Å20.0014 Å20.0016 Å2-0.0522 Å2-0.0119 Å2--0.1043 Å2
L4.4019 °2-0.5987 °2-0.0777 °2-1.4699 °20.1303 °2--2.5017 °2
S0.0237 Å °-0.2141 Å °-0.1115 Å °0.0381 Å °0.0154 Å °0.0217 Å °-0.0301 Å °-0.2997 Å °-0.0391 Å °

+
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