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- PDB-8ovq: Crystal structure of Geodia cydonium sponge adhesion molecule lon... -

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Basic information

Entry
Database: PDB / ID: 8ovq
TitleCrystal structure of Geodia cydonium sponge adhesion molecule long form (SAML).
ComponentsCell recognition molecule, long form
KeywordsIMMUNE SYSTEM / Ig-like / porifera / evolution
Function / homology
Function and homology information


: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cell recognition molecule, long form
Similarity search - Component
Biological speciesGeodia cydonium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLopez-Sagaseta, J. / Urdiciain, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesMargarita Salas Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
Citation
Journal: Commun Biol / Year: 2025
Title: Unusual traits shape the architecture of the Ig ancestor molecule.
Authors: Urdiciain, A. / Madej, T. / Wang, J. / Song, J. / Erausquin, E. / Youkharibache, P. / Lopez-Sagaseta, J.
#1: Journal: Sci Rep / Year: 2025
Title: Severe deviation in protein fold prediction by advanced AI: a case study.
Authors: Lopez-Sagaseta, J. / Urdiciain, A.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell recognition molecule, long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,58117
Polymers24,3951
Non-polymers1,18616
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration assays supports the monomeric state for this protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.080, 41.160, 77.801
Angle α, β, γ (deg.)90.000, 90.009, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cell recognition molecule, long form


Mass: 24394.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Geodia cydonium (invertebrata) / Gene: crml / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U965
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG4000, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.61→77.8 Å / Num. obs: 27255 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.056 / Rrim(I) all: 0.088 / Χ2: 1.02 / Net I/σ(I): 9.3
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1358 / CC1/2: 0.576 / Χ2: 1.03 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSBUILT=20220110data reduction
XDS0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→38.931 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.147 / SU B: 4.543 / SU ML: 0.067 / Average fsc free: 0.968 / Average fsc work: 0.9808 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2027 1317 4.835 %
Rwork0.1509 25920 -
all0.153 --
obs-27237 99.431 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.307 Å20 Å20.021 Å2
2---1.084 Å20 Å2
3---1.391 Å2
Refinement stepCycle: LAST / Resolution: 1.61→38.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 75 137 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121622
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161446
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.6832214
X-RAY DIFFRACTIONr_angle_other_deg0.5541.5613356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.53956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24710206
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.9961050
X-RAY DIFFRACTIONr_chiral_restr0.0740.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
X-RAY DIFFRACTIONr_nbd_refined0.2170.2266
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.21292
X-RAY DIFFRACTIONr_nbtor_refined0.170.2778
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1230.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2109
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.223
X-RAY DIFFRACTIONr_nbd_other0.2250.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.217
X-RAY DIFFRACTIONr_mcbond_it2.2933.028842
X-RAY DIFFRACTIONr_mcbond_other2.2893.028842
X-RAY DIFFRACTIONr_mcangle_it3.1995.4031049
X-RAY DIFFRACTIONr_mcangle_other3.1995.4071050
X-RAY DIFFRACTIONr_scbond_it2.0523.206780
X-RAY DIFFRACTIONr_scbond_other2.0463.188777
X-RAY DIFFRACTIONr_scangle_it2.7635.7741158
X-RAY DIFFRACTIONr_scangle_other2.755.7441153
X-RAY DIFFRACTIONr_lrange_it4.38736.9911722
X-RAY DIFFRACTIONr_lrange_other4.38636.9881723
X-RAY DIFFRACTIONr_rigid_bond_restr4.06633068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.61-1.6520.287900.25119700.25320660.9410.94999.70960.235
1.652-1.6970.238980.2318180.23119190.9670.9699.84370.209
1.697-1.7460.295920.19918290.20319220.9350.97199.9480.174
1.746-1.80.261880.18817400.19118330.9560.97599.72720.161
1.8-1.8590.2341170.16416620.16917820.9660.98299.83160.141
1.859-1.9240.203860.14116550.14417440.9720.98799.8280.119
1.924-1.9960.189750.12415840.12716610.980.99199.87960.108
1.996-2.0770.167940.11915430.12216410.9820.99199.75620.107
2.077-2.1690.197590.11414650.11715270.9780.99299.80350.102
2.169-2.2750.167610.11114120.11314760.9830.99299.79670.102
2.275-2.3980.18580.11613600.11914250.9750.99199.50880.109
2.398-2.5420.231540.12212800.12613370.9690.99199.77560.117
2.542-2.7170.178550.12511970.12812540.9820.99199.84050.123
2.717-2.9340.18610.13111250.13411920.9790.98999.49660.133
2.934-3.2120.213560.1499830.15210510.9660.98698.85820.154
3.212-3.5880.226560.1519270.1559990.9650.98798.39840.159
3.588-4.1370.198520.1497960.1528800.9750.98696.36360.165
4.137-5.0530.146310.1426870.1427360.9860.98797.55440.16
5.053-7.0860.196220.2075530.2065930.9790.97696.96460.233
7.086-38.9310.356120.253340.2523540.9460.95397.74010.285

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