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- PDB-5szp: Protocadherin Gamma B7 extracellular cadherin domains 1-4 P21 cry... -

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Basic information

Entry
Database: PDB / ID: 5szp
TitleProtocadherin Gamma B7 extracellular cadherin domains 1-4 P21 crystal form
ComponentsProtocadherin Gamma B7
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 repeats. ...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 / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / trimethylamine oxide / Protocadherin gamma B7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _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 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 4, 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 Gamma B7
B: Protocadherin Gamma B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87029
Polymers94,5912
Non-polymers2,27927
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-69 kcal/mol
Surface area41730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.813, 45.549, 127.072
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protocadherin Gamma B7 / Protein Pcdhgb7 / Protocadherin gamma B7


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

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Sugars , 2 types, 8 molecules

#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 7
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 24 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.68 % / Description: Plate
Crystal growTemperature: 295 K / Method: batch mode / pH: 8.5
Details: 0.1 M Tris-Cl pH 8.5, 0.2 trimethylamine N-oxide, 5% (v/v) Jeffamine M-600 pH 7.0, 17% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.1→39.95 Å / Num. obs: 17677 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 108.83 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.5
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.585 / % possible all: 99.2

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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: 5SZO

5szo


Resolution: 3.1→19.977 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.62
RfactorNum. reflection% reflection
Rfree0.3098 890 5.17 %
Rwork0.2558 --
obs0.2586 17214 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 114 5 6017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026094
X-RAY DIFFRACTIONf_angle_d0.5858348
X-RAY DIFFRACTIONf_dihedral_angle_d13.2193741
X-RAY DIFFRACTIONf_chiral_restr0.0431026
X-RAY DIFFRACTIONf_plane_restr0.0041108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29350.38441570.3452638X-RAY DIFFRACTION96
3.2935-3.54650.40261490.32882774X-RAY DIFFRACTION99
3.5465-3.9010.39051400.32682460X-RAY DIFFRACTION90
3.901-4.460.30731480.24072770X-RAY DIFFRACTION99
4.46-5.59850.25391490.21832804X-RAY DIFFRACTION99
5.5985-19.97730.26981470.2262878X-RAY DIFFRACTION99
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)
10.9061.0699-0.14342.2086-0.14470.0332-0.0536-0.516-0.21510.65940.09290.062-0.94021.01090.18210.9878-0.1947-0.33621.3986-0.36181.195335.59435.174439.7884
20.83971.0626-0.1051.31310.03711.132-0.12840.10090.1380.04560.01480.00880.081-0.48450.12440.9288-0.0126-0.29521.07980.00420.8932-64.8781-2.9486-47.7272
33.0467-0.60361.02142.9421-0.88562.6353-0.1191-0.31680.06860.490.0807-0.2074-0.25940.17290.06970.35980.03130.02030.3130.02890.55084.1971-1.58559.9217
42.3472-0.19191.76362.36240.28584.4292-0.23760.0270.6469-0.4087-0.01990.5773-0.1484-0.55830.12460.4044-0.0517-0.08060.55960.16550.6649-33.49116.2031-19.8682
53.1331.1212.51581.00971.05692.0281-0.1383-0.3845-0.199-0.0992-0.0473-0.10430.047-0.38920.27410.4703-0.1174-0.00220.63060.06480.6965-39.2607-13.2375-12.2411
61.12090.12120.11551.37420.29433.0752-0.0036-0.08350.16990.19180.1815-0.367-0.5280.1443-0.22730.55820.12540.0460.4559-0.1450.5782-7.393310.294422.7488
71.0394-0.30290.06030.80120.94091.6958-0.18320.6667-0.8148-0.16590.2469-0.0059-0.1483-0.4423-0.07780.7428-0.1295-0.13881.157-0.26690.9537-74.458-25.2142-43.3611
83.78660.47961.11871.9477-0.54331.123-0.99-1.2804-0.42060.21.2906-0.3192-0.67221.2152-0.10771.40320.1588-0.45532.279-0.30161.456525.496621.754355.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:96 )A2 - 96
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:96 )B2 - 96
3X-RAY DIFFRACTION3( CHAIN A AND RESID 97:205 )A97 - 205
4X-RAY DIFFRACTION4( CHAIN B AND RESID 97:205 )B97 - 205
5X-RAY DIFFRACTION5( CHAIN A AND RESID 206:308 )A206 - 308
6X-RAY DIFFRACTION6( CHAIN B AND RESID 208:308 )B208 - 308
7X-RAY DIFFRACTION7( CHAIN A AND RESID 309:410 )A309 - 410
8X-RAY DIFFRACTION8( CHAIN B AND RESID 309:410 )B309 - 410

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