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- PDB-7df2: Crystal structure of a C2 domain protein from Ramazzottius varieo... -

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Basic information

Entry
Database: PDB / ID: 7df2
TitleCrystal structure of a C2 domain protein from Ramazzottius varieornatus
ComponentsC2 domain protein
KeywordsMETAL BINDING PROTEIN / tardigrade / Ca-binding protein / C2 domain
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFukuda, Y. / Inoue, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX191C Japan
Japan Society for the Promotion of Science (JSPS)20K15971 Japan
CitationJournal: Protein Sci. / Year: 2021
Title: Structural insights into a C2 domain protein specifically found in tardigrades.
Authors: Fukuda, Y. / Inoue, T.
History
DepositionNov 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3425
Polymers23,8801
Non-polymers4634
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-33 kcal/mol
Surface area8910 Å2
Unit cell
Length a, b, c (Å)62.916, 62.916, 100.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-594-

HOH

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Components

#1: Protein C2 domain protein


Mass: 23879.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: RvY_00338-1, RvY_00338.1, RvY_00338 / Production host: Escherichia coli (E. coli) / Strain (production host): Suffle T7 / References: UniProt: A0A1D1UCW7
#2: Polysaccharide beta-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 mg per mL protein, 0.1 M calcium chloride dihydrate, 0.1 M Tris pH 6.5, 13% (w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→40.7 Å / Num. obs: 22431 / % possible obs: 98.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 24.29 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.091 / Net I/σ(I): 16.2
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1128 / CC1/2: 0.87 / Rrim(I) all: 1.29

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→40.68 Å / SU ML: 0.1663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1101 4.91 %
Rwork0.1747 21302 -
obs0.1765 22403 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.35 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 26 199 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651510
X-RAY DIFFRACTIONf_angle_d1.03112057
X-RAY DIFFRACTIONf_chiral_restr0.0655224
X-RAY DIFFRACTIONf_plane_restr0.0045275
X-RAY DIFFRACTIONf_dihedral_angle_d30.294227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.2571210.24272569X-RAY DIFFRACTION96.76
1.78-1.870.26931580.20842551X-RAY DIFFRACTION96.96
1.87-1.990.21961320.1932614X-RAY DIFFRACTION97.27
1.99-2.140.22321320.18552617X-RAY DIFFRACTION97.66
2.14-2.360.21741470.18752640X-RAY DIFFRACTION98.06
2.36-2.70.19191210.18582701X-RAY DIFFRACTION98.26
2.7-3.40.21891520.17392704X-RAY DIFFRACTION98.72
3.4-40.680.1971380.15372906X-RAY DIFFRACTION99.12

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