[English] 日本語
Yorodumi
- PDB-4q6j: Crystal Structure of EAL domain Protein from Listeria monocytogen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q6j
TitleCrystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e
ComponentsLmo0131 protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TIM barrel / alpha-betafold
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase activity
Similarity search - Function
EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PHOSPHATE ION / Lmo0131 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.369 Å
AuthorsKim, Y. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e
Authors: Kim, Y. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,79019
Polymers58,6412
Non-polymers1,14917
Water7,080393
1
A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules

A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,58138
Polymers117,2834
Non-polymers2,29834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16100 Å2
ΔGint30 kcal/mol
Surface area39890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.771, 72.483, 77.573
Angle α, β, γ (deg.)90.00, 125.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Lmo0131 protein


Mass: 29320.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0131 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q8YAJ4

-
Non-polymers , 5 types, 410 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.8 M sodium phosphate, 0.8 M postassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
Reflection twinOperator: -h-2*l,-k,l / Fraction: 0.5
ReflectionResolution: 1.37→50 Å / Num. all: 120312 / Num. obs: 120312 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.02 Å2 / Rsym value: 0.083 / Net I/σ(I): 13.1
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4456 / Rsym value: 0.6 / % possible all: 72.2

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1621)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.369→30.069 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: TWIN_LSQ_F
Details: both Freidel pair reflections were used in refinement, which is reflected the refinement statistics
RfactorNum. reflection% reflectionSelection details
Rfree0.169 6111 5.08 %random
Rwork0.137 ---
all0.14 120309 --
obs0.14 120309 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.369→30.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 72 393 4448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134390
X-RAY DIFFRACTIONf_angle_d1.4155927
X-RAY DIFFRACTIONf_dihedral_angle_d15.0031694
X-RAY DIFFRACTIONf_chiral_restr0.089660
X-RAY DIFFRACTIONf_plane_restr0.006762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.3698-1.39340.30852060.25764176438268
1.3934-1.41880.27512740.24775001527580
1.4188-1.44610.25512820.23495598588090
1.4461-1.47560.2313360.21085671600791
1.4756-1.50770.23393050.19475746605192
1.5077-1.54270.21762830.19615819610293
1.5427-1.58130.22132970.19235771606893
1.5813-1.6240.22332900.18975774606493
1.624-1.67180.21613020.18485830613293
1.6718-1.72580.20482950.18625819611493
1.7258-1.78740.20763140.18085832614694
1.7874-1.8590.20113390.1765839617893
1.859-1.94350.18533110.1695835614694
1.9435-2.0460.19393070.16595906621394
2.046-2.17410.17922810.15275893617495
2.1741-2.34180.18123160.14335904622094
2.3418-2.57720.15423440.12545899624394
2.5772-2.94960.1663160.11385949626595
2.9496-3.7140.12363030.09346009631295
3.714-24.23430.12273200.09216001632194

+
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