[English] 日本語
Yorodumi
- PDB-3r1o: Odorant Binding Protein 7 from Anopheles gambiae with Four Disulf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r1o
TitleOdorant Binding Protein 7 from Anopheles gambiae with Four Disulfide Bridges
ComponentsOdorant binding protein, antennal
KeywordsTRANSPORT PROTEIN / all helical protein / odorant molecules binding / mosquito antenna
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular region
Similarity search - Function
: / Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PALMITIC ACID / AGAP001556-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLagarde, A. / Spinelli, S. / Tegoni, M. / Field, L. / He, X. / Zhou, J.J. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of Odorant Binding Protein 7 from Anopheles gambiae Exhibits an Outstanding Adaptability of Its Binding Site.
Authors: Lagarde, A. / Spinelli, S. / Tegoni, M. / He, X. / Field, L. / Zhou, J.J. / Cambillau, C.
History
DepositionMar 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Odorant binding protein, antennal
B: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2564
Polymers28,7432
Non-polymers5132
Water3,441191
1
A: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6282
Polymers14,3721
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6282
Polymers14,3721
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.704, 46.469, 57.438
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Odorant binding protein, antennal / OBP 7 / Odorant-binding protein AgamOBP7


Mass: 14371.638 Da / Num. of mol.: 2 / Fragment: UNP residues 29-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP7, AgamOBP7, AGAP001556, agCG57323 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7PXT9
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 33 mM HEPES, pH 7.25-8.25, 0.4-1.0 M KCl, 6.6 mM sodium borate, 0.83 M sodium citrate tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→55.8 Å / Num. all: 14055 / Num. obs: 14055 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.1
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 8.8 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ERB

2erb


Resolution: 2.1→55.79 Å / Cor.coef. Fo:Fc: 0.8506 / Cor.coef. Fo:Fc free: 0.8403 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT/BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 995 7.19 %RANDOM
Rwork0.2723 ---
obs0.2735 13831 --
all-13831 --
Displacement parametersBiso mean: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.4426 Å20 Å23.2827 Å2
2--1.7811 Å20 Å2
3----1.3385 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.1→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 36 191 1978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091823HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.252463HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d22619SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes343HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3254HARMONIC5
X-RAY DIFFRACTIONt_it01823HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion21.87
X-RAY DIFFRACTIONt_chiral_improper_torsion0251SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02294SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.27 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.4289 201 7.36 %
Rwork0.4252 2529 -
all0.4254 2730 -
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)
10.0905-0.03280.1570.140.16430.40260.001-0.00590.00370.00020.0035-0.0035-0.00110.001-0.00440.01430.0087-0.01630.00820.0097-0.01534.9494-0.08074.8904
20.1974-0.0232-0.03280.0417-0.03280.09480.0007-0.00060.0036-0.0021-0.0003-0.0017-0.0020.0013-0.00040.00430.0066-0.00780.00950.001-0.001911.18312.7701-0.7827
30.1055-0.13870.01660.1370.10610.37470-0.00190.0022-0.0006-0.00140.00130.00240.00120.00140.01110.0051-0.00450.00330.0028-0.0058-1.5823-20.724133.9184
40.09820.0378-0.00210.1199-0.08780.1219-0.0015-0.0010.0061-0.00450.0023-0.00250.00030.0004-0.00080.01050.001-0.01180.00790.0046-0.00875.2174-18.328.4486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|15 - A|82}A15 - 82
2X-RAY DIFFRACTION2{A|92 - A|133}A92 - 133
3X-RAY DIFFRACTION3{B|11 - B|82}B11 - 82
4X-RAY DIFFRACTION4{B|92 - B|133}B92 - 133

+
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