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- PDB-7qr2: Crystal structure of chicken Ovalbumin-related protein X -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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