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- PDB-5szo: Protocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 ... -

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Basic information

Entry
Database: PDB / ID: 5szo
TitleProtocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 crystal form
ComponentsProtocadherin Gamma B7
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / 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
alpha-D-mannopyranose / Protocadherin gamma B7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.612 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Bahna, F. / Honig, B. / Shapiro, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/Office of the DirectorOD012351 United States
National Institutes of Health/Office of the DirectorOD021764 United States
CitationJournal: Elife / Year: 2016
Title: gamma-Protocadherin structural diversity and functional implications.
Authors: Goodman, K.M. / Rubinstein, R. / Thu, C.A. / Mannepalli, S. / Bahna, F. / Ahlsen, G. / Rittenhouse, C. / Maniatis, T. / Honig, B. / Shapiro, L.
History
DepositionAug 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 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 Gamma B7
B: Protocadherin Gamma B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,12129
Polymers94,5912
Non-polymers2,53027
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-66 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.150, 97.150, 312.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe oligomeric state was determined by sedimentation equilibrium analytical ultracentrifugation

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Components

#1: Protein Protocadherin Gamma B7 / Protocadherin Gamma B7 / PcdhgB7


Mass: 47295.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgb7, mCG_133388 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91XX3
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-3-deoxy-Fucp]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
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: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 8.5
Details: 0.1 M Tris-Cl pH 8.5, 0.2 M trimethylamine N-oxide, 3% dextran sulfate sodium salt 5000, 17% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.59→104.13 Å / Num. obs: 18347 / % possible obs: 99.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 109.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.183 / Net I/σ(I): 9
Reflection shellResolution: 3.59→3.93 Å / Redundancy: 12.3 % / Rmerge(I) obs: 3.722 / Mean I/σ(I) obs: 1 / CC1/2: 0.741 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN

4zpl

4zpm

4zpo

4zps

5dzv

5dzx

4zi9

4zi8

5zsm

5szn


Resolution: 3.612→19.93 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 44.17
Details: Ellipsoidal resolution limits were applied to the data due to severe anisotropy. The limits are 4.5/4.5/3.6 angstrom along the a*/b*/c* axes respectively. Completeness with respect to the ...Details: Ellipsoidal resolution limits were applied to the data due to severe anisotropy. The limits are 4.5/4.5/3.6 angstrom along the a*/b*/c* axes respectively. Completeness with respect to the diffracting ellipsoid = 90%.
RfactorNum. reflection% reflection
Rfree0.2787 576 4.84 %
Rwork0.2421 --
obs0.244 11902 66.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.612→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 129 0 6293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036383
X-RAY DIFFRACTIONf_angle_d0.5888729
X-RAY DIFFRACTIONf_dihedral_angle_d13.2683937
X-RAY DIFFRACTIONf_chiral_restr0.0421067
X-RAY DIFFRACTIONf_plane_restr0.0041152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6123-3.97320.4091210.2354483X-RAY DIFFRACTION12
3.9732-4.54220.34141120.28292198X-RAY DIFFRACTION52
4.5422-5.70040.33252060.27414229X-RAY DIFFRACTION99
5.7004-19.93050.24582370.22234416X-RAY DIFFRACTION100

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