[English] 日本語
Yorodumi
- PDB-7tx8: Long form D7 protein from Anopheles darlingi with U46619 and sero... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tx8
TitleLong form D7 protein from Anopheles darlingi with U46619 and serotonin bound
ComponentsLong form D7 salivary protein
KeywordsBLOOD CLOTTING / odorant-binding
Function / homologyresponse to stimulus / Pheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / Chem-PUC / SEROTONIN / Long form D7 salivary protein
Function and homology information
Biological speciesAnopheles darlingi (American malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsAndersen, J.F. / Alvarenga, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Functional aspects of evolution in a cluster of salivary protein genes from mosquitoes.
Authors: Alvarenga, P.H. / Dias, D.R. / Xu, X. / Francischetti, I.M.B. / Gittis, A.G. / Arp, G. / Garboczi, D.N. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionFeb 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Long form D7 salivary protein
B: Long form D7 salivary protein
C: Long form D7 salivary protein
D: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,67512
Polymers139,5684
Non-polymers2,1078
Water2,846158
1
A: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.060, 98.060, 273.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Long form D7 salivary protein


Mass: 34892.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles darlingi (American malaria mosquito)
Production host: Escherichia coli (E. coli) / References: UniProt: B6DDQ8
#2: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-PUC / (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid / 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid


Mass: 350.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H34O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 30% PEG 5000 MME, 0.1 M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→53.31 Å / Num. obs: 53228 / % possible obs: 100 % / Redundancy: 22.06 % / Biso Wilson estimate: 59.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.086 / Χ2: 0.933 / Net I/σ(I): 25.46 / Num. measured all: 1174205 / Scaling rejects: 103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.51-2.5823.120.6396.1289915388938890.9620.653100
2.58-2.6523.0010.5357.2387241379337930.9740.547100
2.65-2.7222.6090.4228.8882590365336530.9840.432100
2.72-2.8121.970.35410.1778543357535750.9870.362100
2.81-2.920.0760.26312.4469483346134610.9920.27100
2.9-323.450.22116.1478839336233620.9950.225100
3-3.1123.6650.1819.0576226322132210.9960.184100
3.11-3.2423.4630.14323.8174285316631660.9970.146100
3.24-3.3823.0610.11728.669438301130110.9980.12100
3.38-3.5522.6120.09932.6565124288028800.9980.102100
3.55-3.7422.2020.08835.7360524272627260.9980.09100
3.74-3.9721.3330.0838.9255615260726070.9990.081100
3.97-4.2418.830.07239.7146622247624760.9990.074100
4.24-4.5821.8730.06944.949390225922580.9990.07100
4.58-5.0222.2350.06746.3647849215221520.9990.069100
5.02-5.6121.8830.06646.1842059192219220.9990.067100
5.61-6.4821.1820.06446.1636751173517350.9990.065100
6.48-7.9419.2790.0645.228147146014600.9990.061100
7.94-11.2319.3010.05747.522833118311830.9990.059100
11.23-53.3118.2390.05645.59127317016980.9990.05899.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.51 Å84.92 Å
Translation2.51 Å84.92 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unliganded AnDar-D7L2

Resolution: 2.51→53.31 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2.35 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 2556 4.87 %
Rwork0.2179 49937 -
obs0.2202 52493 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.89 Å2 / Biso mean: 62.1989 Å2 / Biso min: 33.25 Å2
Refinement stepCycle: final / Resolution: 2.51→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9407 0 308 158 9873
Biso mean--58.82 54.92 -
Num. residues----1176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.560.36191250.3012610273595
2.56-2.610.351420.29792629277195
2.61-2.670.31821390.28392673281296
2.67-2.730.34361590.2772697285697
2.73-2.80.32321570.27182702285997
2.8-2.870.31751770.25842684286199
2.87-2.960.28931430.25592714285798
2.96-3.050.36231260.2622773289999
3.05-3.160.30451320.2672806293899
3.16-3.290.32731310.283227722903100
3.29-3.440.28861150.22327942909100
3.44-3.620.28081520.210928172969100
3.62-3.850.24541310.199127832914100
3.85-4.140.22891500.191628402990100
4.14-4.560.22211330.173328452978100
4.56-5.220.22681480.18628533001100
5.22-6.570.24251430.218329093052100
6.57-53.310.251530.20430363189100
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)
11.315-0.1033-0.82511.55120.69113.81580.17270.0726-0.201-0.068-0.24290.23260.1416-0.22530.0610.26840.0378-0.03810.3653-0.0720.477412.545429.0476-37.8699
21.4196-0.5586-0.13851.3043-1.78384.0789-0.24760.13510.15810.3708-0.075-0.321-0.33470.29070.28730.6038-0.0972-0.13680.38610.02850.5533-31.28360.5553-9.4409
32.26670.1581-0.77921.9448-1.50494.10280.0529-0.0149-0.3095-0.2323-0.1949-0.03070.4079-0.11010.15330.2832-0.0268-0.00110.3494-0.05050.4777-18.411628.0469-58.1677
41.21850.1499-2.11972.0237-0.29454.6846-0.1620.015-0.20380.30610.0067-0.20090.05210.30790.15830.4239-0.1365-0.01960.54750.04920.5233-17.496628.289411.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 297)A3 - 297
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 297)B3 - 297
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 297)C3 - 297
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 297)D3 - 297

+
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://pdbjlc1.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