[English] 日本語
Yorodumi
- PDB-3ljn: Ankyrin repeat protein from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ljn
TitleAnkyrin repeat protein from Leishmania major
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / ankyrin / Structural Genomics / PSI / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / ANK repeat / Protein Structure Initiative
Function / homology
Function and homology information


Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ANK_REP_REGION domain-containing protein / :
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsHolmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Ankyrin repeat protein from Leishmania major
Authors: Merritt, E.A. / Holmes, M.A. / Napuli, A. / Kalyuzhniy, O. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, L.M.J. / Hol, W.G.J.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)41,1221
Polymers41,1221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.293, 85.656, 76.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein hypothetical protein /


Mass: 41122.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ankyrin repeat / Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF29.1100, LMJ_0751 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q4FXU4, UniProt: E9ADW8*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: protein buffer 25 mM HEPES pH 7.5, 100 mM NaCl; crystallization buffer 100 mM NaCl, 100 mM MMT pH 9.0, 22% PEG 2000MME, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97954, 0.97963, 0.95369
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 7, 2005
RadiationProtocol: three wavelength MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.979631
30.953691
ReflectionResolution: 2.9→50 Å / Num. obs: 8482 / % possible obs: 95.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Χ2: 1.348 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-32.40.9287420.91285.9
3-3.1230.5628200.87894.3
3.12-3.273.40.4268321.10897.2
3.27-3.443.60.3298701.23497.9
3.44-3.653.60.2288551.55298.4
3.65-3.943.60.1648551.87897.6
3.94-4.333.60.1198651.4997.4
4.33-4.963.60.0948711.46596.8
4.96-6.243.60.0968661.32795.2
6.24-503.40.0619061.26192.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→45.925 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.219 / ESU R: 1.078 / ESU R Free: 0.479 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2949 455 5.373 %
Rwork0.2287 --
obs-8469 94.944 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.078 Å20 Å20 Å2
2--0.357 Å20 Å2
3----0.279 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 0 0 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222399
X-RAY DIFFRACTIONr_bond_other_d0.0010.021577
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9573258
X-RAY DIFFRACTIONr_angle_other_deg0.86333871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98424.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.561514
X-RAY DIFFRACTIONr_chiral_restr0.0660.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.888-2.9630.421270.31446564576.279
2.963-3.0440.385360.353862691.693
3.044-3.1320.313450.28153460096.5
3.132-3.2280.361200.26256160096.833
3.228-3.3330.317370.25453457998.618
3.333-3.4490.331300.25251455598.018
3.449-3.5790.279290.22150054197.782
3.579-3.7240.265140.22849851998.651
3.724-3.8880.319230.21446550097.6
3.888-4.0770.384250.20944848597.526
4.077-4.2950.272190.2243546597.634
4.295-4.5530.25220.1939743296.991
4.553-4.8640.277220.21936740496.287
4.864-5.2490.356310.24734539096.41
5.249-5.7430.313200.2632736694.809
5.743-6.4080.261100.25230833196.073
6.408-7.3750.19140.22125528694.056
7.375-8.9750.201130.17822725195.618
8.975-12.4570.212120.16217920792.271
12.457-45.9250.34360.28411713889.13
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)
141.6422-9.0298-41.251414.63055.922241.7290.9535-0.30661.18970.35440.29880.6296-1.2583-0.0683-1.25230.79680.1561-0.20120.7784-0.20580.584914.83386.333673.0548
21.9937-0.407-0.53694.8272-0.69683.76150.05010.1107-0.1147-0.0019-0.09670.05060.04070.05030.04660.1959-0.0310.01140.1746-0.01140.224715.67214.024460.4596
32.0963-1.82890.31717.4355-4.57714.318-0.31160.0810.24530.10550.18260.0197-0.16010.17950.1290.3866-0.0001-0.04540.46-0.0440.420912.82067.585645.5793
43.51271.1328-1.33356.8610.71075.7583-0.0985-0.30520.08440.04810.049-0.1793-0.17650.18310.04950.3143-0.0455-0.03470.2654-0.00120.238912.614911.294536.1901
51.1624-0.69280.73553.2164-2.4191.9098-0.02280.1938-0.19920.0964-0.1703-0.36720.06650.22530.19310.50330.0527-0.08860.4003-0.0770.37977.201110.905126.1376
626.4975-9.63255.69378.1877-1.72716.2398-0.123-1.0207-0.8321-0.20050.33520.37180.5131-0.0729-0.21220.5504-0.0143-0.08290.2971-0.01120.42571.31168.958520.1523
75.77341.09610.67514.18420.31023.62910.02490.1335-0.3023-0.0794-0.03250.07670.1313-0.11380.00760.28740.0191-0.01680.14560.00360.1974-2.984919.48978.7102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA12 - 20
2X-RAY DIFFRACTION2ALLA21 - 86
3X-RAY DIFFRACTION3ALLA87 - 132
4X-RAY DIFFRACTION4ALLA133 - 181
5X-RAY DIFFRACTION5ALLA182 - 221
6X-RAY DIFFRACTION6ALLA222 - 237
7X-RAY DIFFRACTION7ALLA238 - 315

+
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