[English] 日本語
Yorodumi
- PDB-6v4c: Culex quinquefasciatus D7 long form 1- CxD7L1 in complex with ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v4c
TitleCulex quinquefasciatus D7 long form 1- CxD7L1 in complex with ADP
ComponentsLong form D7clu1 salivary protein
KeywordsPROTEIN BINDING / mosquito salivary protein / ADP binding / D7 protein
Function / homologyPheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / ADENOSINE-5'-DIPHOSPHATE / 2-ETHOXYETHANOL / DI(HYDROXYETHYL)ETHER / Long form D7clu1 salivary protein
Function and homology information
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsCalvo, E. / Garboczi, D.N. / Martin-Martin, I. / Gittis, A.G.
CitationJournal: Nat Commun / Year: 2020
Title: ADP binding by the Culex quinquefasciatus mosquito D7 salivary protein enhances blood feeding on mammals.
Authors: Martin-Martin, I. / Paige, A. / Valenzuela Leon, P.C. / Gittis, A.G. / Kern, O. / Bonilla, B. / Chagas, A.C. / Ganesan, S. / Smith, L.B. / Garboczi, D.N. / Calvo, E.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Long form D7clu1 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,99213
Polymers33,6551
Non-polymers1,33712
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.660, 84.320, 132.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-311-

ZN

21A-473-

HOH

31A-514-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Long form D7clu1 salivary protein / CxD7L1


Mass: 33655.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito)
Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: Q95V93

-
Non-polymers , 7 types, 133 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate, pH 6.5, 25% 550 PEG MME, 0.01 M Zn sulfate

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→39.02 Å / Num. obs: 30364 / % possible obs: 99.1 % / Redundancy: 5.912 % / Biso Wilson estimate: 51.472 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 1.044 / Net I/σ(I): 12.19 / Num. measured all: 179520 / Scaling rejects: 174
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
1.97-2.025.9480.6432.3513294223522350.8390.705100
2.02-2.085.9320.4323.4513004219321920.9190.474100
2.08-2.145.8960.3184.6212417210621060.950.349100
2.14-2.25.8890.2535.7112013204120400.9670.278100
2.2-2.275.9010.2097.1611903202020170.9730.2399.9
2.27-2.356.0850.1668.9811804194419400.9780.18399.8
2.35-2.446.1570.13910.5911402185218520.9830.153100
2.44-2.546.1180.12412.111080181818110.9880.13699.6
2.54-2.666.0520.10714.0810409173317200.9890.11899.2
2.66-2.796.0340.09515.639848165116320.9910.10598.8
2.79-2.945.9510.08716.889200158115460.9920.09597.8
2.94-3.115.8460.0818.188687151214860.9920.08898.3
3.11-3.335.7530.07319.217951140513820.9930.0898.4
3.33-3.65.750.06920.227383131312840.9930.07597.8
3.6-3.945.7070.06420.676848122512000.9960.0798
3.94-4.415.7720.06121.16366111511030.9960.06798.9
4.41-5.095.7710.05721.1457029949880.9970.06299.4
5.09-6.235.740.05121.1348048398370.9970.05699.8
6.23-8.815.6660.04421.0937456726610.9980.04898.4
8.81-39.0250.03819.7116603973320.9980.04283.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NHT

3nht


Resolution: 1.97→39.02 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 24.33
RfactorNum. reflection% reflection
Rfree0.2349 2000 6.81 %
Rwork0.2136 --
obs0.2151 29350 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.96 Å2 / Biso mean: 56.5121 Å2 / Biso min: 29.09 Å2
Refinement stepCycle: final / Resolution: 1.97→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 80 124 2444
Biso mean--57.35 48.85 -
Num. residues----294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.020.30421270.2622173887
2.02-2.070.24961350.2442184191
2.07-2.130.25331380.2251187793
2.13-2.20.27541380.2348189495
2.2-2.280.24871420.2387194896
2.28-2.370.26841410.2323193297
2.37-2.480.26841450.2466197997
2.48-2.610.28981440.2376198298
2.61-2.780.26861470.2451199298
2.78-2.990.27771460.2416199197
2.99-3.290.24921450.2355198998
3.29-3.770.261480.2112203098
3.77-4.750.17321500.1744205699
4.75-390.22041540.2033210197
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)
11.6220.02110.18291.53210.94830.60770.0249-0.338-0.20930.50290.072-0.46770.65361.08640.01820.57870.316-0.04660.92740.04660.495924.4608-7.4944-16.4741
21.5326-0.35690.39811.7295-0.22431.4937-0.0687-0.2344-0.21640.29640.0857-0.10310.5131-0.132-0.02821.18490.21150.13440.520.09540.743713.8297-22.0125-19.9082
30.35430.05530.02980.08260.09990.1253-0.1076-0.4723-0.35090.25890.2213-0.36130.48950.4312-0.00121.11090.6361-0.05340.99080.02880.902327.9333-21.6703-17.3912
40.81750.13950.00461.64610.38522.3683-0.065-0.114-0.0970.07560.01720.10040.34230.20840.05090.34060.02040.01240.32040.05330.36345.94061.0596-18.2141
51.2563-0.15110.83641.89890.70232.0253-0.049-0.05320.07030.06730.07010.0566-0.06190.11670.01620.35190.022-0.00280.38970.01590.37528.953610.6719-14.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 65 )A2 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 80 )A66 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 118 )A81 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 217 )A119 - 217
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 295 )A218 - 295

+
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