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- PDB-8tnv: Hemocyanin Functional Unit CCHB-g of Concholepas concholepas -

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Basic information

Entry
Database: PDB / ID: 8tnv
TitleHemocyanin Functional Unit CCHB-g of Concholepas concholepas
ComponentsHemocyanin Functional Unit CCHB-g
KeywordsOXYGEN TRANSPORT / Hemocyanin / metalloprotein / copper protein / Concholepas concholepas
Function / homologyBROMIDE ION / CU2-O2 CLUSTER / Chem-PG6
Function and homology information
Biological speciesConcholepas concholepas (barnacle rock-shell)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMunoz, S. / Vallejos-Baccelliere, G. / Manubens, A. / Salazar, M. / Nascimento, A.F.Z. / Ambrosio, A.L.B. / Becker, M.I. / Guixe, V. / Castro-Fernandez, V.
Funding support Chile, 4items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)FAPESP 2019/13318-5 Chile
Comision Nacional Cientifica y Technologica (CONICYT)1191321 Chile
Comision Nacional Cientifica y Technologica (CONICYT)1201200 Chile
Comision Nacional Cientifica y Technologica (CONICYT)EQM 120208 Chile
CitationJournal: Structure / Year: 2024
Title: Structural insights into a functional unit from an immunogenic mollusk hemocyanin.
Authors: Munoz, S.M. / Vallejos-Baccelliere, G. / Manubens, A. / Salazar, M.L. / Nascimento, A.F.Z. / Tapia-Reyes, P. / Meneses, C. / Ambrosio, A.L.B. / Becker, M.I. / Guixe, V. / Castro-Fernandez, V.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Hemocyanin Functional Unit CCHB-g
B: Hemocyanin Functional Unit CCHB-g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,61714
Polymers90,5702
Non-polymers3,04612
Water16,664925
1
A: Hemocyanin Functional Unit CCHB-g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9236
Polymers45,2851
Non-polymers1,6385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemocyanin Functional Unit CCHB-g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6938
Polymers45,2851
Non-polymers1,4087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.682, 103.368, 119.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

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Protein , 1 types, 2 molecules AB

#1: Protein Hemocyanin Functional Unit CCHB-g


Mass: 45285.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Concholepas concholepas (barnacle rock-shell)

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-4/a4-b1_a6-f1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 3 / 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

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Non-polymers , 5 types, 933 molecules

#4: Chemical ChemComp-CUO / CU2-O2 CLUSTER / CU-O2-CU LINKAGE


Mass: 159.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O2
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein condition: Protein 3 mg/mL, 20 mM Imidazole-HCl pH 6.0, and 300 mM NaCl. Reservoir condition: 20% w/V PEGMME 2000 and 150 mM KBr.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.5→47.41 Å / Num. obs: 149523 / % possible obs: 99.92 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1226 / Rpim(I) all: 0.03507 / Rrim(I) all: 0.1276 / Net I/σ(I): 14.47
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 14807 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.3925 / Rrim(I) all: 1.466 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→47.41 Å / SU ML: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.317
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.186 14398 5.01 %
Rwork0.166 --
obs0.169 149416 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6362 0 176 925 7463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116877
X-RAY DIFFRACTIONf_angle_d1.0769352
X-RAY DIFFRACTIONf_dihedral_angle_d14.1172574
X-RAY DIFFRACTIONf_chiral_restr0.07991
X-RAY DIFFRACTIONf_plane_restr0.0111225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2844890.27329196X-RAY DIFFRACTION100
1.52-1.530.26494870.26829098X-RAY DIFFRACTION100
1.53-1.550.27954480.25239159X-RAY DIFFRACTION100
1.55-1.570.27015110.25159095X-RAY DIFFRACTION100
1.57-1.590.27174640.24289126X-RAY DIFFRACTION100
1.59-1.620.24234910.22399109X-RAY DIFFRACTION100
1.62-1.640.25024650.22249145X-RAY DIFFRACTION100
1.64-1.660.26154810.21849138X-RAY DIFFRACTION100
1.66-1.690.23425000.20749082X-RAY DIFFRACTION100
1.69-1.720.23494740.20299135X-RAY DIFFRACTION100
1.72-1.750.2394480.19759108X-RAY DIFFRACTION99
1.75-1.780.2325190.19689110X-RAY DIFFRACTION99
1.78-1.810.22795050.20419038X-RAY DIFFRACTION100
1.81-1.850.22244600.19549171X-RAY DIFFRACTION100
1.85-1.890.21355450.18869045X-RAY DIFFRACTION100
1.89-1.930.21844840.17559098X-RAY DIFFRACTION99
1.93-1.980.19425290.16729071X-RAY DIFFRACTION99
1.98-2.040.19264480.16339142X-RAY DIFFRACTION100
2.04-2.10.18714650.15949156X-RAY DIFFRACTION100
2.1-2.160.18754990.15789135X-RAY DIFFRACTION100
2.16-2.240.17354520.15719127X-RAY DIFFRACTION100
2.24-2.330.18334470.15269130X-RAY DIFFRACTION100
2.33-2.440.18234410.15449125X-RAY DIFFRACTION99
2.44-2.560.18044610.15529125X-RAY DIFFRACTION99
2.56-2.730.16415050.14969071X-RAY DIFFRACTION99
2.73-2.940.17624660.16269056X-RAY DIFFRACTION99
2.94-3.230.18514440.16389097X-RAY DIFFRACTION99
3.23-3.70.17394810.15159022X-RAY DIFFRACTION99
3.7-4.660.14554810.13188995X-RAY DIFFRACTION98
4.66-47.410.15645080.15869065X-RAY DIFFRACTION99

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