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- PDB-6van: Crystal structure of caltubin from the great pond snail -

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Basic information

Entry
Database: PDB / ID: 6van
TitleCrystal structure of caltubin from the great pond snail
ComponentsCaltubin, EF-hand
KeywordsMETAL BINDING PROTEIN / EF-hand / calcium-binding protein / invertebrate / Structural Genomics Consortium / SGC
Function / homologyEF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / STRONTIUM ION / Calcium-binding protein
Function and homology information
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.33 Å
AuthorsDong, A. / Li, A. / Zhang, Q. / Barszczyk, A. / Chern, Y.H. / Arrowsmith, C.H. / Edwards, A.M. / Zhong, Z.P. / Tong, Y. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)RN314068-377078 Canada
CitationJournal: to be published
Title: Cell-penetrating caltubin promotes neurite outgrowth and regrowth through calcium-dependent microtubule regulation
Authors: Dong, A. / Li, A. / Zhang, Q. / Barszczyk, A. / Chern, Y.H. / Arrowsmith, C.H. / Edwards, A.M. / Zhong, Z.P. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Caltubin, EF-hand
B: Caltubin, EF-hand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,46923
Polymers32,9432
Non-polymers1,52621
Water5,693316
1
A: Caltubin, EF-hand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,23511
Polymers16,4721
Non-polymers76310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caltubin, EF-hand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,23512
Polymers16,4721
Non-polymers76311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.026, 32.632, 85.955
Angle α, β, γ (deg.)90.000, 105.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Caltubin, EF-hand / Calcium-binding protein


Mass: 16471.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pRARE2 / References: UniProt: Q2VA57
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24% PEG 3350, 0.1M Tris pH7.5, 150 mM SrCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 58175 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.031 / Rrim(I) all: 0.063 / Χ2: 0.934 / Net I/σ(I): 8.6 / Num. measured all: 232691
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.353.90.64328200.7630.3670.7420.45695.9
1.35-1.384.10.56528250.7980.3140.6490.48796.1
1.38-1.44.10.49828280.860.2770.5710.4796.5
1.4-1.4340.42828520.8710.2410.4920.47696.6
1.43-1.463.90.35428650.8910.2050.4110.48796.6
1.46-1.53.90.2928620.9350.1670.3350.52396.7
1.5-1.5440.24928750.9510.1390.2860.52697.5
1.54-1.583.80.20228560.9650.1170.2350.54797
1.58-1.624.10.1729060.9710.0940.1950.55697.5
1.62-1.684.10.13928530.9780.0770.1590.59697.4
1.68-1.744.10.11228910.9870.0620.1280.62797.2
1.74-1.813.90.08929380.9910.0520.1040.67598.2
1.81-1.894.10.07728940.9940.0430.0880.77298.2
1.89-1.9940.06229400.9960.0350.0720.93298.6
1.99-2.114.10.05229280.9960.0290.061.12598.8
2.11-2.274.20.04929510.9970.0270.0561.36898.8
2.27-2.53.90.04529900.9970.0260.0521.52499.3
2.5-2.874.10.04629720.9960.0260.0521.79199.4
2.87-3.6140.04230350.9970.0240.0492.06899.4
3.61-503.80.0430940.9970.0230.0462.49499.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
SOLVE2.13phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.33→45.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.08 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1868 3.2 %RANDOM
Rwork0.1906 ---
obs0.1916 56295 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.44 Å2 / Biso mean: 17.401 Å2 / Biso min: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20.09 Å2
2--0.84 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.33→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 28 326 2648
Biso mean--27.66 28.91 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132548
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172212
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6553485
X-RAY DIFFRACTIONr_angle_other_deg1.4691.5875163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70923.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5821513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02561
LS refinement shellResolution: 1.33→1.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 116 -
Rwork0.262 3973 -
all-4089 -
obs--93.68 %

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