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- PDB-6pgw: Crystal structure of zebrafish Protocadherin-19 EC3-6 -

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Basic information

Entry
Database: PDB / ID: 6pgw
TitleCrystal structure of zebrafish Protocadherin-19 EC3-6
ComponentsProtocadherin-19
KeywordsCELL ADHESION / protocadherin / Pcdh19 / epilepsy / calcium-binding
Function / homology
Function and homology information


regulation of neuronal action potential / neural tube formation / brain morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / anatomical structure morphogenesis / visual perception / excitatory postsynaptic potential / cell-cell adhesion / postsynapse / cell adhesion ...regulation of neuronal action potential / neural tube formation / brain morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / anatomical structure morphogenesis / visual perception / excitatory postsynaptic potential / cell-cell adhesion / postsynapse / cell adhesion / cadherin binding / calcium ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Wu:fc83e05 protein / Protocadherin-19
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCooper, S.R. / Hudson, J.D. / Sotomayor, M.
CitationJournal: Structure / Year: 2021
Title: A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and potential protein interaction sites.
Authors: Hudson, J.D. / Tamilselvan, E. / Sotomayor, M. / Cooper, S.R.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,21611
Polymers48,8321
Non-polymers38410
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-51 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.920, 58.896, 70.956
Angle α, β, γ (deg.)90.00, 117.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protocadherin-19


Mass: 48832.059 Da / Num. of mol.: 1 / Fragment: UNP residues 227-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pcdh19, wu:fc83e05 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1L1W7, UniProt: F8W3X3*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 100 mM HEPES, 55% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10543 / % possible obs: 86.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.066 / Rrim(I) all: 0.102 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 411 / CC1/2: 0.917 / Rpim(I) all: 0.198 / Rrim(I) all: 0.304 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IU9

5iu9


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.836 / SU B: 62.373 / SU ML: 0.506 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29815 482 5.4 %RANDOM
Rwork0.21485 ---
obs0.21939 8441 85.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.816 Å2
Baniso -1Baniso -2Baniso -3
1--8.11 Å2-0 Å2-1.23 Å2
2--0.19 Å2-0 Å2
3---5.91 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 10 18 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193418
X-RAY DIFFRACTIONr_bond_other_d0.0030.023040
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.964578
X-RAY DIFFRACTIONr_angle_other_deg0.81437065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57925.776161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17515543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9571514
X-RAY DIFFRACTIONr_chiral_restr0.090.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213785
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
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_it2.1575.1041722
X-RAY DIFFRACTIONr_mcbond_other2.1145.1031715
X-RAY DIFFRACTIONr_mcangle_it3.5977.6572132
X-RAY DIFFRACTIONr_mcangle_other3.5967.6582133
X-RAY DIFFRACTIONr_scbond_it1.9915.2141696
X-RAY DIFFRACTIONr_scbond_other1.9915.2141697
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3087.7842447
X-RAY DIFFRACTIONr_long_range_B_refined7.27996.58613394
X-RAY DIFFRACTIONr_long_range_B_other7.27996.58313394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 30 -
Rwork0.295 573 -
obs--78.21 %
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)
12.5346-1.19460.14961.8218-0.14181.16180.0210.31760.0611-0.1672-0.0619-0.03360.0296-0.09960.0410.0576-0.00780.02410.0579-0.00270.11-82.561326.6345-34.7839
23.0208-0.03082.050.01960.04211.6187-0.1006-0.21430.01550.03160.02460.0090.034-0.01760.0760.06280.04510.03560.13030.08110.1221-46.24397.7517-9.7066
33.0782-0.11870.90890.0644-0.05131.91890.06860.25040.1927-0.0223-0.0787-0.0203-0.10650.01280.01010.01970.03180.00150.09290.04940.18270.3785.16869.6752
43.4346-0.89141.03170.8769-0.11830.5040.0648-0.0459-0.05530.04580.03160.05460.0958-0.0537-0.09640.0954-0.02160.03570.01410.0210.12442.9043-11.2427.1619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A214 - 316
2X-RAY DIFFRACTION1A1007 - 1008
3X-RAY DIFFRACTION1A1016
4X-RAY DIFFRACTION2A317 - 423
5X-RAY DIFFRACTION2A1009 - 1011
6X-RAY DIFFRACTION3A424 - 532
7X-RAY DIFFRACTION3A1012 - 1014
8X-RAY DIFFRACTION4A533 - 640
9X-RAY DIFFRACTION4A1015

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