[English] 日本語
Yorodumi
- PDB-4mir: The structure of Brucella abortus PliC in the hexagonal crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mir
TitleThe structure of Brucella abortus PliC in the hexagonal crystal form
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE INHIBITOR / lysozyme
Function / homologyC-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor / C-type lysozyme inhibitor superfamily / Lipocalin / Beta Barrel / Mainly Beta / membrane / C-type lysozyme inhibitor domain-containing protein
Function and homology information
Biological speciesBrucella abortus bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHa, N.C. / Um, S.H. / Kim, J.S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis for the inhibition of human lysozyme by PliC from Brucella abortus
Authors: Um, S.H. / Kim, J.S. / Kim, K. / Kim, N. / Cho, H.S. / Ha, N.C.
History
DepositionSep 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,9413
Polymers31,9413
Non-polymers00
Water2,360131
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3120 Å2
ΔGint-23 kcal/mol
Surface area10120 Å2
MethodPISA
2
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-22 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.395, 58.395, 364.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-253-

HOH

-
Components

#1: Protein Putative uncharacterized protein


Mass: 10646.972 Da / Num. of mol.: 3 / Fragment: UNP residues 27-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus bv. 1 (bacteria) / Strain: 9-941 / Gene: BruAb1_0462 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57ES7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.0M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 5, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 15664 / Num. obs: 15422 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.44197.5
2.44-2.49198
2.49-2.53198.7
2.53-2.58198.6
2.58-2.64198.2
2.64-2.7198.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.752 Å / SU ML: 0.35 / σ(F): 1.52 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 764 4.96 %RANDOM
Rwork0.2072 ---
obs0.2103 15406 99.04 %-
all-15555 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 131 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082242
X-RAY DIFFRACTIONf_angle_d1.1553041
X-RAY DIFFRACTIONf_dihedral_angle_d15.226809
X-RAY DIFFRACTIONf_chiral_restr0.073359
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.5850.33871420.2566280999
2.585-2.84440.29261640.2396280799
2.8444-3.25440.31661550.224289099
3.2544-4.09420.25631560.1915291999
4.0942-19.7530.2311470.1883217100

+
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