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- PDB-6bx7: Crystal Structure of Human Protocadherin-1 EC1-4 -

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Basic information

Entry
Database: PDB / ID: 6bx7
TitleCrystal Structure of Human Protocadherin-1 EC1-4
ComponentsProtocadherin-1
KeywordsCELL ADHESION / cadherins / adhesion / calcium-binding protein / asthma
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / cell-cell junction / cell junction / cell-cell signaling / nervous system development / cell adhesion / intracellular membrane-bounded organelle / calcium ion binding / nucleolus / nucleoplasm / plasma membrane
Similarity search - Function
Protocadherin / Protocadherin / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Protocadherin / Protocadherin / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsModak, D. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateAlfred P. Sloan FR-2015-65794 United States
CitationJournal: Commun Biol / Year: 2019
Title: Identification of an adhesive interface for the non-clustered delta 1 protocadherin-1 involved in respiratory diseases.
Authors: Modak, D. / Sotomayor, M.
History
DepositionDec 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48113
Polymers49,8021
Non-polymers67912
Water45025
1
A: Protocadherin-1
hetero molecules

A: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,96226
Polymers99,6042
Non-polymers1,35824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4850 Å2
ΔGint-118 kcal/mol
Surface area46740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.981, 146.981, 147.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protocadherin-1 / Cadherin-like protein 1 / Protocadherin-42 / PC42


Mass: 49801.922 Da / Num. of mol.: 1 / Fragment: Cadherin domains 1-4, residues 58-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH1 / Plasmid: PET21A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08174
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium Chloride, 0.1 M HEPES Sodium Salt pH 7.5, 15% PEG 400 + 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 22567 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.05 / Rrim(I) all: 0.164 / Net I/σ(I): 18.3
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.627 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 1103 / CC1/2: 0.716 / Rpim(I) all: 0.521 / Rrim(I) all: 1.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DZV

5dzv


Resolution: 2.85→48.26 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.155 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.279 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24336 1120 5 %RANDOM
Rwork0.22097 ---
obs0.22213 21392 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.792 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: 1 / Resolution: 2.85→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 26 25 3339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172996
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6664569
X-RAY DIFFRACTIONr_angle_other_deg0.8861.6417065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97624.098183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94415557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4431521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
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_it2.0964.4741713
X-RAY DIFFRACTIONr_mcbond_other2.0684.471712
X-RAY DIFFRACTIONr_mcangle_it3.6086.72136
X-RAY DIFFRACTIONr_mcangle_other3.6116.7062137
X-RAY DIFFRACTIONr_scbond_it1.9144.7491640
X-RAY DIFFRACTIONr_scbond_other1.9134.751640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2577.0342434
X-RAY DIFFRACTIONr_long_range_B_refined8.7384.15613155
X-RAY DIFFRACTIONr_long_range_B_other8.72984.15213146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.851→2.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 91 -
Rwork0.338 1517 -
obs--99.01 %
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)
12.4115-1.1832-2.76724.11574.68556.60410.3065-0.3730.56790.10340.0894-0.0897-0.52570.0926-0.39580.69680.1459-0.09990.6092-0.06750.475557.682221.597760.3586
20.49970.35261.10570.41341.65828.21350.0233-0.02540.01250.03370.0215-0.09680.03620.1392-0.04480.17140.0207-0.0740.011-0.02060.287865.5707-0.406722.8339
32.4852.56153.08813.08324.10666.2596-0.06480.1388-0.0107-0.2620.07040.0197-0.3143-0.0704-0.00560.170.00110.01960.03720.01470.133448.3599-18.5947-19.7646
40.4853-0.1094-0.66740.82230.85737.55910.07420.441-0.0077-0.59860.020.0776-0.14560.0721-0.09420.5939-0.0613-0.04430.5364-0.05590.353238.6049-37.4569-62.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 106
2X-RAY DIFFRACTION1A502 - 503
3X-RAY DIFFRACTION2A107 - 218
4X-RAY DIFFRACTION2A504 - 506
5X-RAY DIFFRACTION3A219 - 325
6X-RAY DIFFRACTION3A507 - 509
7X-RAY DIFFRACTION4A326 - 439
8X-RAY DIFFRACTION4A510 - 511

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