[English] 日本語
Yorodumi
- PDB-3o6n: Crystal Structure of APL1 leucine-rich repeat domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o6n
TitleCrystal Structure of APL1 leucine-rich repeat domain
ComponentsAPL1
KeywordsPROTEIN BINDING / leucine-rich repeat
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBaxter, R.H.G. / Steinert, S. / Chelliah, Y. / Volohonsky, G. / Levashina, E.A. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae.
Authors: Baxter, R.H. / Steinert, S. / Chelliah, Y. / Volohonsky, G. / Levashina, E.A. / Deisenhofer, J.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9974
Polymers45,1301
Non-polymers8673
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.770, 70.350, 161.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There is one biological unit in the asymmetric unit (chain A and chain B).

-
Components

#1: Protein APL1


Mass: 45130.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: APL1 / Production host: Trichoplusia ni (cabbage looper)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 16% PEG 8000, 0.1M NaCl, 0.1M Na-Hepes, 0.2M Calcium acetate, pH 7.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionHighest resolution: 1.49 Å / Num. obs: 56125 / % possible obs: 76.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.642 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.72
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.49-1.530.0130.72984130624.7
1.53-1.570.0131.25390187836.1
1.57-1.620.0131.77826222143.5
1.62-1.670.0132.410370250351.2
1.67-1.720.0133.413386285659.5
1.72-1.780.0134.416631320669.2
1.78-1.850.0135.720621359879.9
1.85-1.920.0137.827582419198
1.92-2.010.01311.330087412599.1
2.01-2.110.01314.928652392499.6
2.11-2.220.01317.627541377699.4
2.22-2.360.0132125836354899.4
2.36-2.520.01323.824645338999.6
2.52-2.720.01326.922758314499.7
2.72-2.980.01330.521082293999.7
2.98-3.330.01333.518722262799.6
3.33-3.850.01337.216618237399.6
3.85-4.720.01338.213605201399.7
4.72-6.670.01337.910617159799.3
6.670.01336.8563791194.3

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.796 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.2 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1924 5 %RANDOM
Rwork0.1692 ---
obs0.1708 38467 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.535 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 109.01 Å2 / Biso mean: 26.5874 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1-13.6059 Å2-0 Å2-0 Å2
2---5.592 Å20 Å2
3----8.0139 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 56 384 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033296
X-RAY DIFFRACTIONf_angle_d0.7914504
X-RAY DIFFRACTIONf_chiral_restr0.054532
X-RAY DIFFRACTIONf_plane_restr0.003580
X-RAY DIFFRACTIONf_dihedral_angle_d13.9081238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.24481310.1882480261197
1.8963-1.94760.20451350.17442598273399
1.9476-2.00490.22791340.16392563269799
2.0049-2.06960.2041350.15582555269099
2.0696-2.14360.16321360.15112588272499
2.1436-2.22940.19241360.153925722708100
2.2294-2.33080.18971360.159425932729100
2.3308-2.45370.21571380.16172604274299
2.4537-2.60740.21221380.167126372775100
2.6074-2.80870.2171380.176326042742100
2.8087-3.09130.21061380.183326262764100
3.0913-3.53840.19231410.178926672808100
3.5384-4.45730.17191400.14826682808100
4.4573-42.80710.19961480.18162788293698
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)
10.73890.3533-0.04970.42960.391.0660.1364-0.3558-0.05920.2863-0.0495-0.03340.52520.4036-0.07640.28730.1003-0.03540.3895-0.05780.14679.545173.638741.1392
20.83550.0013-0.20850.34480.18091.2868-0.0499-0.15880.1140.0320.0770.049-0.01770.052-0.00240.12190.0268-0.01260.1306-0.05010.14534.52480.49921.6631
30.3803-0.1433-0.4970.65430.20720.61880.02250.02180.1186-0.0325-0.02880.0179-0.007-0.063-0.00010.08890.0044-0.00840.09630.00340.1216.774773.8815-4.0702
40.2898-0.2345-0.2711.13410.68030.6734-0.01260.04150.0095-0.17080.0568-0.0628-0.0111-0.0192-0.04810.1028-0.0078-0.00440.05590.00160.041512.532859.2852-17.662
50.3602-0.16690.10450.3386-0.06390.19680.0580.0435-0.2397-0.0495-0.0680.03170.217-0.1106-0.0320.2227-0.0325-0.02410.1732-0.03590.1810.368741.5941-20.9485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 140:192)A140 - 192
2X-RAY DIFFRACTION2(chain A and resid 193:317)A193 - 317
3X-RAY DIFFRACTION3(chain A and resid 318:397)A318 - 397
4X-RAY DIFFRACTION4(chain A and resid 398:485)A398 - 485
5X-RAY DIFFRACTION5(chain A and resid 486:523)A486 - 523

+
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