[English] 日本語
Yorodumi
- PDB-2ar1: Structure of Hypothetical protein from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ar1
TitleStructure of Hypothetical protein from Leishmania major
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyEVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / nucleus / Alpha Beta / EVE domain-containing protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.
Authors: Arakaki, T. / Le Trong, I. / Phizicky, E. / Quartley, E. / DeTitta, G. / Luft, J. / Lauricella, A. / Anderson, L. / Kalyuzhniy, O. / Worthey, E. / Myler, P.J. / Kim, D. / Baker, D. / Hol, W.G. / Merritt, E.A.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.description / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE Author states that residue 139 is indeed an ARG. There is a sequence error at Genbank ...SEQUENCE Author states that residue 139 is indeed an ARG. There is a sequence error at Genbank database, gi:68130356.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4432
Polymers20,3511
Non-polymers921
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.199, 64.607, 72.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-325-

HOH

-
Components

#1: Protein hypothetical protein


Mass: 20351.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF36.6870 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q067
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.8 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0 ul protein 8.2 mg/ml 1.0 ul crystallization buffer 2.8 M Na Malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-3 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 19933 / Num. obs: 18997 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.041 / Χ2: 1.077 / Net I/σ(I): 10.068
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsΧ2Diffraction-ID
1.6-1.6594.60.6931.60315580.9551
1.65-1.795.10.55215280.9021
1.7-1.7693.90.4052.79115181.0521
1.76-1.8393.80.3223.46315641.0691
1.83-1.9192.60.2294.77114931.0591
1.91-2.0292.40.1526.60915001.0761
2.02-2.1493.30.0999.20315331.1461
2.14-2.3196.30.07711.46616021.2611
2.31-2.5497.50.0613.95816241.1731
2.54-2.9198.70.04417.44616541.111
2.91-3.6698.90.0322.91816760.9951
3.66-5096.20.02131.85217471.1221

-
Phasing

Phasing MRRfactor: 0.505 / Cor.coef. Fo:Fc: 0.373
Highest resolutionLowest resolution
Rotation3 Å29.51 Å
Translation3 Å29.51 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.6data extraction
MOLREPphasing
REFMACrefmac_5.2.0005 24/04/2001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution MAD structure

Resolution: 1.602→29.514 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.425 / SU ML: 0.107 / SU R Cruickshank DPI: 0.103 / SU Rfree: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.106 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 974 5.128 %random
Rwork0.185 ---
all0.187 18995 --
obs0.187 18995 94.913 %-
Displacement parametersBiso mean: 19.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.517 Å20 Å20 Å2
2--0.395 Å20 Å2
3----0.912 Å2
Refinement stepCycle: LAST / Resolution: 1.602→29.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 6 99 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221332
X-RAY DIFFRACTIONr_bond_other_d0.0050.021200
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9481796
X-RAY DIFFRACTIONr_angle_other_deg0.91732791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25723.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5531512
X-RAY DIFFRACTIONr_chiral_restr0.1180.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.220.2270
X-RAY DIFFRACTIONr_nbd_other0.2090.21232
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2640
X-RAY DIFFRACTIONr_nbtor_other0.0880.2765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3140.222
X-RAY DIFFRACTIONr_mcbond_it2.55921006
X-RAY DIFFRACTIONr_mcbond_other0.5812314
X-RAY DIFFRACTIONr_mcangle_it2.50631268
X-RAY DIFFRACTIONr_mcangle_other1.22831087
X-RAY DIFFRACTIONr_scbond_it3.9364655
X-RAY DIFFRACTIONr_scbond_other1.7741147
X-RAY DIFFRACTIONr_scangle_it5.1756528
X-RAY DIFFRACTIONr_scangle_other2.57361704
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 (%)
1.602-1.6440.333660.2661238146688.95
1.644-1.6890.351530.2581262139194.536
1.689-1.7380.284650.2461229137793.972
1.738-1.7910.287720.2281183133294.219
1.791-1.8490.261700.2281148130393.477
1.849-1.9140.31640.2141079123792.401
1.914-1.9860.277560.2031072121992.535
1.986-2.0670.253610.1961043117893.718
2.067-2.1580.271500.185989111493.268
2.158-2.2630.267600.191985108696.225
2.263-2.3840.221480.184947102796.884
2.384-2.5280.265560.18889797797.544
2.528-2.7010.191410.19987493597.861
2.701-2.9150.205430.18582086599.769
2.915-3.1910.203350.17175779899.248
3.191-3.5620.235390.16468272899.038
3.562-4.1030.165390.16160765798.326
4.103-5.0010.193240.14553857198.424
5.001-6.9730.268200.18542545298.451
6.973-29.5140.163120.19224630086
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)
11.2296-0.01640.1062.57260.23442.4287-0.01420.13130.06670.296-0.02110.0352-0.00820.05510.0354-0.1305-0.00550.0055-0.10040.01830.2169-0.93918.53914.085
20.8165-0.28090.07371.2407-0.02681.64560.00380.13790.06120.0852-0.0399-0.0591-0.03810.07650.0361-0.1596-0.0196-0.0033-0.0710.01170.24150.61119.7439.764
31.0139-0.67751.24962.30830.20964.7760.00810.08480.06160.07260.0163-0.0875-0.01050.1402-0.0244-0.1815-0.0161-0.0025-0.04160.00890.2636-0.62316.4727.118
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
117 - 3715 - 45
2238 - 12746 - 135
33128 - 163136 - 171

+
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://pdbjlvh1.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