[English] 日本語
Yorodumi
- PDB-7qr2: Crystal structure of chicken Ovalbumin-related protein X -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qr2
TitleCrystal structure of chicken Ovalbumin-related protein X
ComponentsOvalbumin-related protein X
KeywordsANTIMICROBIAL PROTEIN / chicken egg / serpin / innate immunity / heparin binding protein
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / heparin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Ovalbumin-related protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsCoste, F. / Rehault-Godbert, S.
Funding support France, 1items
OrganizationGrant numberCountry
Other governmentMUSE (Region Centre) France
CitationJournal: To Be Published
Title: Crystal structure of chicken Ovalbumin-related protein X
Authors: Coste, F. / Rehault-Godbert, S.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ovalbumin-related protein X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0528
Polymers45,4811
Non-polymers5707
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-35 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.742, 64.275, 115.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Ovalbumin-related protein X


Mass: 45481.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: OVALX / Production host: Escherichia coli (E. coli) / References: UniProt: R9TNA6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: phosphate/citrate buffer, LiSO4, PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.64→56.167 Å / Num. obs: 49372 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 17.5
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2417 / CC1/2: 0.894 / Rpim(I) all: 0.279 / Rrim(I) all: 0.731 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVA

1ova


Resolution: 1.64→33.03 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 2492 5.05 %
Rwork0.1765 46863 -
obs0.178 49355 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.37 Å2
Refinement stepCycle: LAST / Resolution: 1.64→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 32 202 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992915
X-RAY DIFFRACTIONf_angle_d1.05493962
X-RAY DIFFRACTIONf_chiral_restr0.0675463
X-RAY DIFFRACTIONf_plane_restr0.0079498
X-RAY DIFFRACTIONf_dihedral_angle_d12.20771044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.670.34011420.30242551X-RAY DIFFRACTION99.04
1.67-1.710.32321610.28012503X-RAY DIFFRACTION99.25
1.71-1.750.29561280.24642563X-RAY DIFFRACTION98.79
1.75-1.790.26451130.22312613X-RAY DIFFRACTION99.45
1.79-1.830.23981330.20182548X-RAY DIFFRACTION99.44
1.83-1.880.23311320.19132547X-RAY DIFFRACTION99.08
1.88-1.940.2161390.17982603X-RAY DIFFRACTION99.31
1.94-20.19961420.19012572X-RAY DIFFRACTION99.49
2-2.070.29131240.18972595X-RAY DIFFRACTION99.63
2.07-2.150.20731510.17742587X-RAY DIFFRACTION99.67
2.15-2.250.221250.17612591X-RAY DIFFRACTION99.6
2.25-2.370.22141310.16982614X-RAY DIFFRACTION99.71
2.37-2.520.19851460.17612592X-RAY DIFFRACTION99.78
2.52-2.710.23721370.17912642X-RAY DIFFRACTION99.75
2.71-2.980.20671590.1682609X-RAY DIFFRACTION99.96
2.98-3.410.17221320.17152658X-RAY DIFFRACTION99.89
3.42-4.30.18961710.15462642X-RAY DIFFRACTION99.75
4.3-33.030.17411260.17262833X-RAY DIFFRACTION99.6
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)
18.22135974287-3.584057396880.8655722669262.26512264266-0.7863210108334.448821433730.09202569944770.120377763344-0.3111695872120.0592403666457-0.193005311179-0.0068890467820.6798148096240.107201010570.117181851950.249844761761-0.01922201063240.01026282366520.144324699932-0.006887051681350.228280059372-10.4124516601-0.572773990286-11.0790824956
21.685586730340.309010448307-1.180613671480.3769335694860.0364729341764.53474836638-0.103951538473-0.203492117745-0.2288117941340.0861315153126-0.002557832719510.03016299721860.4534644342980.1773936489140.006028110331790.2196919053440.01811585604490.03003967661970.14023188728-0.007471741444950.275868856077-8.687671625420.390932591198-1.79745921059
31.101581726630.8421988559930.5132315874371.75140036654-0.8959770376572.91083952745-0.0161980762807-0.206957406408-0.317035224443-0.2164783873770.135761148699-0.3287301490750.5866030168141.100267726220.08431236855340.2669625442740.1190959269980.03016919541160.405220799291-0.03212901967610.3646865726565.424432676512.81170360343-5.91393175914
42.595637685531.37743002836-0.5111081669141.92739711666-1.180871213363.654949786290.0936960949256-0.4717575302770.1466601086040.23275654036-0.08854015741620.0382807467787-0.2986950635020.2646131564670.00333447198120.159714384536-0.007213348893570.01967855661180.280733322312-0.06873441574430.2586199233881.0230160956614.32121311962.77053164373
56.86322381334-0.0122540579421.266317887785.83542229681-2.701806216275.186187937180.1191416110520.7596988698891.06786829905-0.7159655144390.259602572791-0.109131475381-0.3195290940920.254776197674-0.3555766000870.500827720678-0.0223154872060.1076622667340.343717426343-0.04611679998980.210691598235-5.3202985285116.9443840435-33.3273616951
64.345414517360.3671978722280.06122006645315.251194949150.2132992521213.883077253730.1443131383440.5192805316110.0619509898724-0.1224865807040.0652334777819-0.410150410865-0.1191734807060.0166010704196-0.2067616606830.279720903109-0.02023098713550.01664577368820.2473189516920.01245494664190.130505078045-6.010687302127.78191845705-34.0747913068
71.725428888090.241741050520.1881529189881.742856501771.07893187634.952536927440.08999669360120.201445983131-0.1639999271-0.1702146119560.0695228929881-0.0675971181920.346839714329-0.161907099753-0.1477925966870.255321919754-0.0314348445583-0.02432422556470.1850027490740.02032115689770.234054944656-8.045588625153.58003943905-26.3404039392
82.41149001797-0.1425401434820.1869305489341.92669895261-1.243054144195.58152055247-0.012215661163-0.37516814395-0.006409014480090.16377251697-0.0387019799191-0.0155905564865-0.007629231273830.02952346698440.05677491149880.1567436049180.007872197673060.02088344774910.195701838447-0.01135930309350.209912072397-12.42095809465.919388049337.72624038017
91.69206226416-0.0505858496665-0.4931188711560.7630229453610.004712430143193.532582299490.06569705096660.290153860094-0.00731296728296-0.2094094833810.123373583434-0.053715000672-0.08297094225360.261317452374-0.1431829152040.167820425142-0.01939946062130.01183531098680.12611162973-0.01360438972130.169831364719-4.80083301288.27532069367-22.4509165169
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 8 through 31 )8 - 311 - 24
22chain 'A' and (resid 32 through 91 )32 - 9125 - 70
33chain 'A' and (resid 92 through 123 )92 - 12371 - 102
44chain 'A' and (resid 124 through 198 )124 - 198103 - 177
55chain 'A' and (resid 199 through 219 )199 - 219178 - 198
66chain 'A' and (resid 220 through 240 )220 - 240199 - 219
77chain 'A' and (resid 241 through 307 )241 - 307220 - 286
88chain 'A' and (resid 308 through 337 )308 - 337287 - 316
99chain 'A' and (resid 338 through 402 )338 - 402317 - 365

+
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