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- PDB-3zzo: Crystal structure of the CG11501 protein in P212121 spacegroup -

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Basic information

Entry
Database: PDB / ID: 3zzo
TitleCrystal structure of the CG11501 protein in P212121 spacegroup
ComponentsCG11501
KeywordsIMMUNE SYSTEM / IMMUNE RESPONSE
Function / homology
Function and homology information


immune system process / cytokine activity / response to bacterium / defense response to virus / extracellular space
Similarity search - Function
Alpha-Beta Plaits - #2800 / Diedel / Diedel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Protein Diedel
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.15 Å
AuthorsCoste, F. / Roussel, A.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Diedel, a Marker of the Immune Response of Drosophila Melanogaster.
Authors: Coste, F. / Kemp, C. / Bobezeau, V. / Hetru, C. / Kellenberger, C. / Imler, J.-L. / Roussel, A.
History
DepositionSep 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG11501
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7043
Polymers10,5841
Non-polymers1202
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.916, 44.576, 59.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG11501 / RH38110P


Mass: 10583.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PMT/V5-HIS A / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9VAK8
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE MUTATION S75P SEEN IN THE CRYSTAL STRUCTURE MIGHT BE DUE TO AN ERROR INTO THE SEQUENCE DATABASE

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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: 1.83 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growpH: 5.5 / Details: 50MM NA-ACETATE PH5.5, 200MM NASCN, 18-25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 25, 2008 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 1.15→19 Å / Num. obs: 28072 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.15→18 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.875 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15129 1422 5.1 %RANDOM
Rwork0.12892 ---
obs0.13006 26611 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.15→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 7 144 862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022756
X-RAY DIFFRACTIONr_bond_other_d0.0180.02521
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9371023
X-RAY DIFFRACTIONr_angle_other_deg1.32531260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.869596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.08124.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35315124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.229156
X-RAY DIFFRACTIONr_chiral_restr0.1310.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02863
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02157
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5181.5466
X-RAY DIFFRACTIONr_mcbond_other0.6441.5195
X-RAY DIFFRACTIONr_mcangle_it2.2232746
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2023290
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2594.5275
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.53831277
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 95 -
Rwork0.201 1860 -
obs--94.81 %
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)
10.89560.4099-0.08710.1298-0.03670.61490.0035-0.0518-0.0499-0.0045-0.0127-0.0170.01550.03460.00920.04880.0015-0.00050.06330.00710.041715.35419.63219.029
20.7476-0.13461.07140.1662-0.11941.62360.0274-0.0122-0.041-0.0101-0.00460.00130.0317-0.0175-0.02290.0474-0.0005-0.00050.05660.00050.03912.09416.9438.38
30.7283-0.13860.78280.0211-0.10451.2497-0.02760.0619-0.007-0.0034-0.00830.0052-0.07530.06450.0360.0521-0.0053-0.00250.06010.00130.03482.03423.658-0.725
47.63912.16987.538621.492611.55966.15910.38640.3859-0.55870.31230.2243-0.48890.47460.3124-0.61070.1412-0.0094-0.0770.084-0.03780.05590.41412.017-1.778
50.97230.27480.46160.46210.42130.4149-0.00060.0083-0.00560.00410.0092-0.01340.00510.009-0.00850.0485-0.00230.00240.05750.00260.03457.38221.8119.007
60.54150.0532-0.0320.0797-0.0210.1763-0.0033-0.0452-0.01590.00410.00280.00760.0013-0.00050.00050.04710.00080.00190.06030.00170.037121.77923.77416.734
71.38470.310.05860.0761-0.00570.19160.0115-0.08040.0278-0.0013-0.00410.006-0.0042-0.0052-0.00740.04520.00140.00040.0614-0.00470.03849.31326.88618.014
80.4412-0.24330.20990.343-0.09470.1458-0.00490.01090.0174-0.0053-0.0177-0.009-0.0050.00310.02260.04760.0004-0.00030.0569-0.00030.0380.3228.87210.8
90.2677-0.34920.35070.9584-0.62451.0393-0.0078-0.0094-0.0175-0.0251-0.0114-0.0178-0.031-0.03180.01920.05040.00250.00220.0535-0.00160.0335-2.68421.8046.769
102.9223-2.56421.58137.2552-3.0841.2961-0.04220.0670.09060.0985-0.06-0.2278-0.03890.03120.10220.0463-0.00170.00350.0510.00230.03818.34811.04518.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 30
2X-RAY DIFFRACTION2A31 - 36
3X-RAY DIFFRACTION3A37 - 48
4X-RAY DIFFRACTION4A49 - 53
5X-RAY DIFFRACTION5A54 - 65
6X-RAY DIFFRACTION6A66 - 84
7X-RAY DIFFRACTION7A85 - 93
8X-RAY DIFFRACTION8A94 - 101
9X-RAY DIFFRACTION9A102 - 110
10X-RAY DIFFRACTION10A111 - 117

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