[English] 日本語
Yorodumi
- PDB-7kcg: Salivary protein from Culex quiquefasciatus that belongs to the C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kcg
TitleSalivary protein from Culex quiquefasciatus that belongs to the Cysteine and Tryptophan-Rich (CWRC) family
Components16 kDa salivary peptide
KeywordsUNKNOWN FUNCTION / Salivary protein / Culex quinquefasciatus / Cysteine and Tryptophan-Rich (CWRC) protein family
Function / homologyRicin-type beta-trefoil lectin domain-like / Ricin B, lectin domain / Ricin B-like lectins / transferase activity / FORMIC ACID / 16 kDa salivary peptide
Function and homology information
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGarboczi, N.D. / Gittis, A.G. / Kern, O. / Martin-Martin, I. / Calvo, E.
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: The structures of two salivary proteins from the West Nile vector Culex quinquefasciatus reveal a beta-trefoil fold with putative sugar binding properties
Authors: Kern, O. / Valenzuela Leon, P.C. / Gittis, A.G. / Bonilla, B. / Cruz, P. / Chagas, A.C. / Ganesan, S. / Ribeiro, J.M. / Garboczi, D.N. / Martin-Martin, I. / Calvo, E.
History
DepositionOct 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16 kDa salivary peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6064
Polymers16,4671
Non-polymers1383
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.800, 59.680, 85.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein 16 kDa salivary peptide


Mass: 16467.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6TRZ5
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4M Sodium formate (Condition 33, Crystal Screen, Hampton Research)

-
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: 1.87→34.74 Å / Num. obs: 15256 / % possible obs: 99.6 % / Redundancy: 7.418 % / Biso Wilson estimate: 37.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.041 / Χ2: 1.05 / Net I/σ(I): 23.77 / Num. measured all: 113172 / Scaling rejects: 108
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
1.87-1.924.8480.3673.485231112410790.9480.4196
1.92-1.977.7610.315.798203105710570.9840.332100
1.97-2.037.7470.2437.228212106010600.9880.26100
2.03-2.097.6970.1719.867889102510250.9930.184100
2.09-2.167.6480.12312.697656100110010.9960.132100
2.16-2.247.6680.09516.1572929519510.9970.102100
2.24-2.327.7820.08318.8373709479470.9980.089100
2.32-2.418.0070.07820.7370148768760.9980.083100
2.41-2.528.0020.06624.369548698690.9980.07100
2.52-2.647.9630.05828.9566178318310.9980.062100
2.64-2.797.7870.05131.8861287877870.9980.055100
2.79-2.967.6780.04435.4358357607600.9990.047100
2.96-3.167.4790.03840.3954227257250.9990.041100
3.16-3.417.4080.03842.8647936476470.9990.041100
3.41-3.747.3150.03543.844556096090.9990.038100
3.74-4.187.1910.03144.57403456256110.03399.8
4.18-4.837.2330.03145.8736385035030.9990.033100
4.83-5.917.0280.03244.7530154304290.9990.03499.8
5.91-8.366.8520.0314424053513510.9990.033100
8.36-34.745.3670.02938.8710092051880.9990.03291.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology

Resolution: 1.87→34.74 Å / SU ML: 0.2219 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 32.006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 1187 8 %
Rwork0.2287 13646 -
obs0.2308 14833 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.13 Å2
Refinement stepCycle: LAST / Resolution: 1.87→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 9 30 1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941157
X-RAY DIFFRACTIONf_angle_d1.35981561
X-RAY DIFFRACTIONf_chiral_restr0.0942157
X-RAY DIFFRACTIONf_plane_restr0.0058203
X-RAY DIFFRACTIONf_dihedral_angle_d15.7592394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.960.30881300.28871494X-RAY DIFFRACTION86.84
1.96-2.060.34511420.29551636X-RAY DIFFRACTION94.98
2.06-2.190.32511460.27561671X-RAY DIFFRACTION96.55
2.19-2.360.32591480.26231702X-RAY DIFFRACTION97.99
2.36-2.590.30321500.29081730X-RAY DIFFRACTION99.1
2.59-2.970.27611540.28611764X-RAY DIFFRACTION99.79
2.97-3.740.25251540.22851777X-RAY DIFFRACTION100
3.74-34.740.21321630.1821872X-RAY DIFFRACTION99.17
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)
11.65470064154-0.1787511351670.9819701777081.02508910580.5757674152542.487887173720.03372878888170.368328699576-0.183147087781-1.282215791080.247017070794-0.340929111934-0.02898843862110.5179792559980.008673620834390.47979989468-0.06824831087880.06030452701060.455494773681-0.05603969234470.46498473151524.818707394636.209819845323.2267707036
22.141172653030.2436054225351.636128720072.947010305381.433670933862.5260550497-0.258233678937-0.0363852883580.287802664994-0.6659925272940.120575581576-0.595703660866-1.828813178640.959803894218-0.03004455949070.762762587529-0.1489157595970.07359797197160.471817898744-0.03332768564780.44798636616125.897689548647.751763388129.5321677417
30.589623272164-0.5912600657970.2612166835840.7816395536820.2161152923551.07561134506-0.174346015289-0.30219638503-0.2367774958460.08320031637890.391041939852-0.01297823997430.4635847018510.1560432557530.01340298436670.282019421297-0.0362709602156-0.01521209573090.4485735250690.0121167726910.39288159618322.274617130437.652156372336.8757581785
40.79976974935-0.973713240651.584919139241.20797267751-1.91451862713.12538100614-0.3108210062550.172476378826-0.229645053868-0.2719527836460.423416287197-0.420824371084-1.093374377380.335327106312-0.02119548931110.381390293894-0.1515779897790.06163295958390.39375214374-0.1534316287410.43795853793525.348122329646.650197592934.3813741895
54.227536767490.02654202671832.448732834851.388307046391.86300059833.94235465667-0.4644564486570.6885603693551.45137618363-0.618984801810.03880004428340.478487246792-2.1618318057-0.0397190140585-0.1505585889660.7708910781680.0961239091004-0.1163494728190.384827968684-0.02395345254320.6023620505514.979460882752.397430983732.2491811153
62.318020584190.4937101577190.2287693211782.24608704371-1.831342222981.66913184741-0.0523730490562-0.169651066199-0.131723632396-0.3904199139580.0170308543006-0.229419782361-0.208121315981-0.0643815001753-0.00175367767170.186797894910.02306916707860.01665344068360.349885675368-0.02292161344750.35909408419218.800519405339.058365292233.6475485201
70.1434306650770.084972767372-0.1891988535110.5448006979740.01870384593110.220243474811-0.1057106944370.151981678113-0.00665538114049-0.58550375207-0.128962215420.292149786534-0.302862255283-0.496650098891-0.02397607269310.3350611727160.0460473401893-0.07944166649750.416587082889-0.07461112046960.38164815911712.731605068640.364960841329.6057746261
80.558292913448-0.20045391952-0.3607504241871.22781560610.3031700343710.229337776459-0.07621321906760.5280124898580.138624668352-1.29364321445-0.06636700811630.0539989029784-0.671580746631-0.632501490905-0.02606114464940.6629297522490.0272227558934-0.09741212851680.6902103373180.0128765678150.44946321426912.774644189845.497295865821.2943279496
91.43521170208-0.06537421236680.3150614698061.221231708350.6747876238980.402393020084-0.4639013646850.968945758173-0.162717169502-1.010300168840.233175037917-0.187984421964-0.6727400474490.410700280021-0.009590215732170.413429991983-0.00411842966326-0.04949556939980.419844045759-0.0982002317380.41354173876220.789039464835.861607780522.244774741
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 23 )-1 - 231 - 25
22chain 'A' and (resid 24 through 49 )24 - 4926 - 51
33chain 'A' and (resid 50 through 57 )50 - 5752 - 59
44chain 'A' and (resid 58 through 66 )58 - 6660 - 68
55chain 'A' and (resid 67 through 79 )67 - 7969 - 81
66chain 'A' and (resid 80 through 102 )80 - 10282 - 104
77chain 'A' and (resid 103 through 116 )103 - 116105 - 118
88chain 'A' and (resid 117 through 131 )117 - 131119 - 133
99chain 'A' and (resid 132 through 141 )132 - 141134 - 143

+
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