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- PDB-5szr: Protocadherin Gamma B2 extracellular cadherin domains 3-6 -

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Open data


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Basic information

Entry
Database: PDB / ID: 5szr
TitleProtocadherin Gamma B2 extracellular cadherin domains 3-6
ComponentsProtein Pcdhgb2
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion / 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 B2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Bahna, F. / Rubinstein, R. / 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: Atomic model / Data collection ...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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_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.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 2.3Oct 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: Protein Pcdhgb2
B: Protein Pcdhgb2
C: Protein Pcdhgb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,84962
Polymers144,5353
Non-polymers8,31459
Water4,972276
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A: Protein Pcdhgb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14823
Polymers48,1781
Non-polymers2,97022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein Pcdhgb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90019
Polymers48,1781
Non-polymers2,72218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein Pcdhgb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,80020
Polymers48,1781
Non-polymers2,62219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.755, 104.755, 352.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe protein molecule is a dimer in solution, as determined by analytical ultracentrifugation, however it appears to be monomeric in this crystal structure.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Protein Pcdhgb2 / Protocadherin gamma B2 / Protocadherin gamma subfamily B / 2


Mass: 48178.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: EC domains 3-6 from PcdhgB2 with a C-terminal octahistidine tag
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgb2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91XX7

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Sugars , 4 types, 27 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
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-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar...
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 21
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

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Non-polymers , 3 types, 308 molecules

#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 11.5% (w/v) PEG8000, 23% (v/v) ethylene glycol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1 M Morpheus Buffer System 1 (Mes/Imidazole buffer; Molecular Dimensions) pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 87920 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.886 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.882 / % possible all: 99.9

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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: 5DZV

5dzv


Resolution: 2.3→19.949 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 4279 4.95 %
Rwork0.2499 --
obs0.2513 86452 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9549 0 486 276 10311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410255
X-RAY DIFFRACTIONf_angle_d0.6514045
X-RAY DIFFRACTIONf_dihedral_angle_d15.2876244
X-RAY DIFFRACTIONf_chiral_restr0.0461741
X-RAY DIFFRACTIONf_plane_restr0.0041791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.47391420.44572741X-RAY DIFFRACTION98
2.3261-2.35340.44551290.43412665X-RAY DIFFRACTION99
2.3534-2.38210.48751670.41742722X-RAY DIFFRACTION99
2.3821-2.41220.44211390.40422662X-RAY DIFFRACTION98
2.4122-2.44390.46421450.38382704X-RAY DIFFRACTION98
2.4439-2.47730.38141480.38532655X-RAY DIFFRACTION98
2.4773-2.51260.44081190.37722720X-RAY DIFFRACTION98
2.5126-2.55010.38681630.36232672X-RAY DIFFRACTION98
2.5501-2.58980.39831370.35672658X-RAY DIFFRACTION97
2.5898-2.63220.42311390.33852699X-RAY DIFFRACTION97
2.6322-2.67750.38461290.33052710X-RAY DIFFRACTION98
2.6775-2.7260.37841310.32562703X-RAY DIFFRACTION98
2.726-2.77830.34951530.32352712X-RAY DIFFRACTION98
2.7783-2.83490.35991480.31082706X-RAY DIFFRACTION98
2.8349-2.89640.36011360.30722724X-RAY DIFFRACTION98
2.8964-2.96350.34771260.30872723X-RAY DIFFRACTION98
2.9635-3.03740.31791410.29812706X-RAY DIFFRACTION98
3.0374-3.11920.34371270.29542715X-RAY DIFFRACTION98
3.1192-3.21060.35261290.29052735X-RAY DIFFRACTION98
3.2106-3.31380.33361420.29412726X-RAY DIFFRACTION98
3.3138-3.43170.32661680.27442724X-RAY DIFFRACTION99
3.4317-3.56830.27681490.25632743X-RAY DIFFRACTION98
3.5683-3.72970.24231500.24582760X-RAY DIFFRACTION99
3.7297-3.9250.24551530.21292761X-RAY DIFFRACTION99
3.925-4.16880.22571410.20252800X-RAY DIFFRACTION99
4.1688-4.48730.20421480.17412819X-RAY DIFFRACTION99
4.4873-4.93270.20751400.17972830X-RAY DIFFRACTION99
4.9327-5.63230.18991460.18642834X-RAY DIFFRACTION99
5.6323-7.04380.19331490.21022870X-RAY DIFFRACTION98
7.0438-19.94930.2291450.19362974X-RAY DIFFRACTION97
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)
15.4755-0.5969-1.55265.87591.40351.6636-0.1249-0.1733-0.20240.07610.0319-0.2780.36870.43540.07630.57550.09620.00230.6614-0.03590.400334.3388-7.5392116.5979
25.65250.4143-1.6095.49981.1756.26010.10660.54050.5282-0.2244-0.08930.1422-1.0226-0.4956-0.04670.5990.04830.09680.6010.01960.4838-7.3334.6693-2.7242
33.68340.4631.21353.07230.32763.9919-0.0454-0.6703-0.61340.5439-0.40660.06181.43410.52560.42211.29660.15770.07831.26630.27510.741445.897418.5275140.7285
41.2023-0.13852.4861.2028-2.14268.1122-0.1963-0.28070.14190.3174-0.0414-0.0746-0.83740.4380.25930.89150.07030.0010.75450.03810.463623.09964.5672.8306
51.1688-0.21230.80191.9127-2.43336.5984-0.09440.1999-0.0527-0.1537-0.009-0.12-0.23630.63690.1020.73240.146-0.10130.7798-0.07710.46744.542723.182440.8509
63.0568-0.36510.10592.4027-1.60896.8023-0.068-0.3905-0.1810.37750.0495-0.2527-0.12320.4130.02420.3773-0.01720.01650.48540.00220.376756.480129.298498.1551
71.4657-0.1934-1.92092.5536-1.77429.51920.01510.2544-0.0977-0.25450.14490.07650.3745-0.208-0.1950.5507-0.1004-0.0180.5523-0.01350.397723.55778.637121.4777
83.29830.22992.65491.95881.60517.51790.3602-0.4478-0.16160.0542-0.19430.22210.5062-1.4008-0.19820.4735-0.1224-0.00750.73520.03130.46898.054123.949992.1262
91.8354-0.8516-2.97990.83972.24979.20680.27280.11430.2355-0.19790.0389-0.0374-0.4931-0.5239-0.28060.55720.05290.05970.6707-0.02750.383660.930128.861347.1702
102.2141-0.3893-0.66633.0996-0.74893.24330.00810.3430.0647-0.14340.03650.0833-0.288-0.07090.02020.5397-0.06210.03240.692-0.03540.356535.163930.5847-21.0312
113.9894-0.31570.15942.80190.73865.83180.0072-0.63810.01210.52810.0103-0.0768-0.30050.39650.01530.6171-0.0720.09890.5938-0.00790.37730.440835.2099134.6106
124.94240.645-0.06833.79890.06164.46220.10970.26490.0728-0.24420.066-0.1451-0.03080.2616-0.16820.4502-0.07680.04560.2523-0.02990.292782.932917.71774.4637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 209:310 )A209 - 310
2X-RAY DIFFRACTION2( CHAIN B AND RESID 209:310 )B209 - 310
3X-RAY DIFFRACTION3( CHAIN C AND RESID 210:310 )C210 - 310
4X-RAY DIFFRACTION4( CHAIN A AND RESID 311:415 )A311 - 415
5X-RAY DIFFRACTION5( CHAIN B AND RESID 311:415 )B311 - 415
6X-RAY DIFFRACTION6( CHAIN C AND RESID 311:415 )C311 - 415
7X-RAY DIFFRACTION7( CHAIN A AND RESID 416:525 )A416 - 525
8X-RAY DIFFRACTION8( CHAIN B AND RESID 416:525 )B416 - 525
9X-RAY DIFFRACTION9( CHAIN C AND RESID 416:525 )C416 - 525
10X-RAY DIFFRACTION10( CHAIN A AND RESID 526:637 )A526 - 637
11X-RAY DIFFRACTION11( CHAIN B AND RESID 526:637 )B526 - 637
12X-RAY DIFFRACTION12( CHAIN C AND RESID 526:637 )C526 - 637

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