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- PDB-7qrn: Crystal structure of Ovalbumin-related protein X (OVAX) complexed... -

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Basic information

Entry
Database: PDB / ID: 7qrn
TitleCrystal structure of Ovalbumin-related protein X (OVAX) complexed with fondaparinux
ComponentsOvalbumin-related protein X
KeywordsANTIMICROBIAL PROTEIN / chicken egg / serpin / innate immunity / heparin binding protein / fondaparinux
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
fondaparinux / Ovalbumin-related protein X
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsCoste, F. / Bruneau, G. / Rehault-Godbert, S.
Funding support France, 1items
OrganizationGrant numberCountry
Other governmentMUSE France
CitationJournal: Front Immunol / Year: 2022
Title: Antimicrobial Proteins and Peptides in Avian Eggshell: Structural Diversity and Potential Roles in Biomineralization.
Authors: Moreau, T. / Gautron, J. / Hincke, M.T. / Monget, P. / Rehault-Godbert, S. / Guyot, N.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)47,84213
Polymers45,4811
Non-polymers2,36112
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-42 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)53.504, 68.069, 108.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1508.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: fondaparinux
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: phosphate/citrate, LiSO4, PEG 1500

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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: 1.83→57.66 Å / Num. obs: 35271 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Net I/σ(I): 17.9
Reflection shellResolution: 1.832→1.863 Å / Redundancy: 5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1691 / CC1/2: 0.801 / Rpim(I) all: 0.385 / Rrim(I) all: 0.883 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
autoPROCdata reduction
PHASERphasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVA

1ova


Resolution: 1.83→38.09 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 1733 4.92 %
Rwork0.1772 33517 -
obs0.179 35250 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.46 Å2 / Biso mean: 44.9539 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 1.83→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 140 123 3065
Biso mean--67.97 48.67 -
Num. residues----364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.890.29971450.2732703284899
1.89-1.950.261120.2182792290499
1.95-2.020.23361500.20592755290599
2.02-2.10.26731620.19172712287499
2.1-2.190.25861570.17582761291899
2.19-2.310.2271400.170827932933100
2.31-2.450.21521330.17832791292499
2.45-2.640.20391620.17872785294799
2.64-2.910.22521430.181328002943100
2.91-3.330.2251420.17212825296799
3.33-4.190.17831480.15832844299299
4.19-38.090.20281390.1792956309598
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)
11.80521.0543-0.99670.7392-0.19064.6737-0.0909-0.1522-0.16270.09090.0583-0.00660.6259-0.0226-0.05220.2510.02890.0370.1848-0.01980.2846-7.42750.6333-4.6001
22.01481.34760.70812.8098-0.72213.8333-0.0298-0.1783-0.13330.00860.0361-0.1099-0.03030.4780.00790.1610.01430.01340.3886-0.04340.34814.074511.48050.218
32.84210.04131.75422.9414-3.01915.72380.30180.82280.4248-0.5515-0.0476-0.19640.2171.0142-0.31440.46250.04740.0420.6164-0.01420.3898-2.981117.5813-33.7772
40.96230.2598-0.24140.95520.07474.9519-0.00180.1610.0006-0.17730.11170.00610.08450.1841-0.09260.1516-0.00070.00080.1845-0.01260.2451-6.09976.6422-19.9621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 89 )A8 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 198 )A90 - 198
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 219 )A199 - 219
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 402 )A220 - 402

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