[English] 日本語
Yorodumi
- PDB-9j01: Crystal Structure Sensory Appendage Protein 2 from Anopheles culi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j01
TitleCrystal Structure Sensory Appendage Protein 2 from Anopheles culicifacies
ComponentsChemosensory protein 3
KeywordsLIPID BINDING PROTEIN / Sensory Appendage Protein 2 / SAP2 / Mosquito / Olfaction / hydrophobic chemicals / Vector Control
Function / homologyInsect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / : / Chemosensory protein 3
Function and homology information
Biological speciesAnopheles culicifacies (mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.611 Å
AuthorsGoswami, R. / Biswas, S. / Barbosa, R.L. / Sung, S. / Marquez, J.A. / Chakraborti, S. / Manickam, Y.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
Indian Council of Medical Research75/20/2020/ECD-II India
CitationJournal: To Be Published
Title: Crystal Structure Sensory Appendage Protein 2 from Anopheles culicifacies
Authors: Goswami, R. / Biswas, S. / Barbosa, R.L. / Sung, S. / Marquez, J.A. / Chakraborti, S. / Manickam, Y.
History
DepositionAug 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemosensory protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7868
Polymers13,1531
Non-polymers6337
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-6 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.365, 37.075, 41.014
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Chemosensory protein 3


Mass: 13152.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles culicifacies (mosquito) / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): DL21 (DE3) / References: UniProt: A0A182MAD2
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Lithium chloride, 0.1M Sodium acetate pH 4.5, 36% v/v PEG 400, 0.05M Cadmium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9654 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9654 Å / Relative weight: 1
ReflectionResolution: 1.61→37.08 Å / Num. obs: 12010 / % possible obs: 97.3 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Χ2: 0.91 / Net I/σ(I): 11.8 / Num. measured all: 74827
Reflection shellResolution: 1.61→1.67 Å / % possible obs: 73.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.355 / Num. measured all: 4064 / Num. unique obs: 880 / CC1/2: 0.576 / Rpim(I) all: 0.68 / Rrim(I) all: 1.525 / Χ2: 0.76 / Net I/σ(I) obs: 0.9

-
Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
Aimlessdata scaling
CRANK2phasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.611→31.316 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 604 5.04 %
Rwork0.1881 --
obs0.1906 11986 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.611→31.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms747 0 7 69 823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012768
X-RAY DIFFRACTIONf_angle_d1.1611035
X-RAY DIFFRACTIONf_dihedral_angle_d3.008475
X-RAY DIFFRACTIONf_chiral_restr0.07112
X-RAY DIFFRACTIONf_plane_restr0.007135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.611-1.77280.30841290.27672594X-RAY DIFFRACTION89
1.7728-2.02930.23761580.19552899X-RAY DIFFRACTION100
2.0293-2.55650.19951580.19472914X-RAY DIFFRACTION100
2.5565-31.3160.24781590.17482975X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.9985 Å / Origin y: -3.48 Å / Origin z: -10.0047 Å
111213212223313233
T0.1961 Å20.0035 Å20.0141 Å2-0.196 Å20.0004 Å2--0.2023 Å2
L0.4457 °20.646 °20.3575 °2-1.0656 °20.7236 °2--2.1849 °2
S-0.0038 Å °0.0936 Å °0.0574 Å °-0.0816 Å °-0.0184 Å °0.0889 Å °-0.091 Å °-0.0848 Å °0.004 Å °
Refinement TLS groupSelection details: 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