[English] 日本語
Yorodumi
- PDB-4m0m: The crystal structure of a functionally unknown protein lpg2422 f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m0m
TitleThe crystal structure of a functionally unknown protein lpg2422 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #80 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #430 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #440 / Domain of unknown function DUF5621 / Domain of unknown function (DUF5621) / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Alpha/Beta hydrolase fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DUF5621 domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.192 Å
AuthorsTan, K. / Li, H. / Clancy, S. / Shuman, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein lpg2422 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Tan, K. / Li, H. / Clancy, S. / Shuman, H. / Joachimiak, A.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6726
Polymers87,9001
Non-polymers7735
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.528, 69.234, 177.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative uncharacterized protein


Mass: 87899.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg2422 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: Q5ZSU4
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium Acetate, 0.1M Sodium Cacodylate:HCl, 40% PEG300, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. all: 43629 / Num. obs: 43629 / % possible obs: 99.1 % / Observed criterion σ(F): -5 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2037 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.192→33.975 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2196 5.05 %random
Rwork0.1854 ---
obs0.1882 43522 98.55 %-
all-43522 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.192→33.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 46 82 5897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075929
X-RAY DIFFRACTIONf_angle_d0.9798001
X-RAY DIFFRACTIONf_dihedral_angle_d14.4832263
X-RAY DIFFRACTIONf_chiral_restr0.066867
X-RAY DIFFRACTIONf_plane_restr0.0041051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1918-2.23950.34521190.28732245X-RAY DIFFRACTION87
2.2395-2.29150.29271430.26422423X-RAY DIFFRACTION95
2.2915-2.34880.28641250.24792555X-RAY DIFFRACTION99
2.3488-2.41230.29181430.23882559X-RAY DIFFRACTION100
2.4123-2.48330.31651470.2262582X-RAY DIFFRACTION100
2.4833-2.56340.32351370.21732619X-RAY DIFFRACTION100
2.5634-2.6550.27861330.212575X-RAY DIFFRACTION100
2.655-2.76130.25311240.20162604X-RAY DIFFRACTION100
2.7613-2.88690.26121320.21072617X-RAY DIFFRACTION100
2.8869-3.0390.27061460.20332578X-RAY DIFFRACTION100
3.039-3.22930.27281380.21142613X-RAY DIFFRACTION100
3.2293-3.47840.23561550.19512614X-RAY DIFFRACTION100
3.4784-3.8280.24611260.17822651X-RAY DIFFRACTION100
3.828-4.38090.19471270.14792651X-RAY DIFFRACTION100
4.3809-5.51560.18281440.15022671X-RAY DIFFRACTION100
5.5156-33.97920.23021570.17162769X-RAY DIFFRACTION98
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)
11.52960.0137-0.43910.944-0.09832.59520.01840.13920.0379-0.0482-0.00860.0324-0.1126-0.1415-0.00840.26060.0084-0.02740.40350.01280.279610.516823.6221156.3675
22.1531-0.41111.00931.8732-1.55834.8610.0678-0.08220.0209-0.1467-0.07090.01060.29030.11620.03360.36-0.00250.02950.5090.01450.34289.824210.2415186.2404
32.2924-0.5219-1.1390.35530.02941.5155-0.0744-0.0036-0.339-0.04320.0690.04670.30990.36840.02290.44320.0366-0.02870.4557-0.04480.417229.9917-7.4625163.1511
42.0196-2.78710.89724.2845-1.94891.47810.30580.56170.3184-0.7121-0.432-0.62790.3670.3910.19620.50870.0510.08750.89270.02540.507334.299511.7839137.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 323 )
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 396 )
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 628 )
4X-RAY DIFFRACTION4chain 'A' and (resid 629 through 737 )

+
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