[English] 日本語
Yorodumi
- PDB-2icg: Crystal structure of a protein of unknown function (NP_472245.1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2icg
TitleCrystal structure of a protein of unknown function (NP_472245.1) from Listeria innocua at 1.65 A resolution
ComponentsLin2918 protein
KeywordsStructural Genomics/Unknown function / NP_472245.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homology
Function and homology information


SMI1-KNR4 cell-wall / SMI1/KNR4-like / SMI1/KNR4-like / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_472245.1) from Listeria Innocua at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lin2918 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7603
Polymers17,6281
Non-polymers1322
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.030, 100.030, 62.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-171-

HOH

21A-199-

HOH

31A-200-

HOH

41A-227-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Lin2918 protein


Mass: 17628.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: NP_472245.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q926X2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 277 K / pH: 9
Details: 1.6M (NH4)2SO4, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94926,0.97925
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949261
20.979251
ReflectionResolution: 1.65→29.501 Å / Num. obs: 22770 / % possible obs: 99.6 % / Biso Wilson estimate: 30.934 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.65-1.710.011171.3520000360297.8
1.71-1.780.7642.221192379387.9
1.78-1.860.5852.921261378991
1.86-1.960.3984.322151395691.4
1.96-2.080.266.322149395296.4
2.08-2.240.1848.822811406696.4
2.24-2.460.1231222790406197.8
2.46-2.820.09215.523941426499.2
2.820.07321.423432422699.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.501 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.053 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (6) THERE ARE UNMODELED DENSITIES IN BETWEEN GLU49 AND GLU150.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1165 5.1 %RANDOM
Rwork0.198 ---
obs0.2 22751 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.603 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0.85 Å20 Å2
2---1.69 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 6 172 1398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221277
X-RAY DIFFRACTIONr_bond_other_d0.0010.02848
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9771731
X-RAY DIFFRACTIONr_angle_other_deg0.94732092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96725.55654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.049153
X-RAY DIFFRACTIONr_chiral_restr0.090.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.2060.2244
X-RAY DIFFRACTIONr_nbd_other0.1910.2829
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2637
X-RAY DIFFRACTIONr_nbtor_other0.0890.2634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.213
X-RAY DIFFRACTIONr_mcbond_it2.3833885
X-RAY DIFFRACTIONr_mcbond_other0.6113335
X-RAY DIFFRACTIONr_mcangle_it3.0851302
X-RAY DIFFRACTIONr_scbond_it5.0788513
X-RAY DIFFRACTIONr_scangle_it6.78411426
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 89 -
Rwork0.314 1544 -
obs-1633 98.91 %
Refinement TLS params.Method: refined / Origin x: 30.0119 Å / Origin y: 19.1068 Å / Origin z: 1.7073 Å
111213212223313233
T-0.0596 Å20.0317 Å2-0.0071 Å2--0.0827 Å20.0325 Å2---0.0819 Å2
L3.4547 °20.4112 °20.3844 °2-0.414 °20.1322 °2--1.4191 °2
S-0.0854 Å °0.0228 Å °-0.3628 Å °-0.0097 Å °0.0859 Å °0.1361 Å °-0.0146 Å °-0.0179 Å °-0.0005 Å °
Refinement TLS groupSelection: ALL

+
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