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- PDB-4zpm: Crystal Structure of Protocadherin Alpha C2 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 4zpm
TitleCrystal Structure of Protocadherin Alpha C2 EC1-3
ComponentsProtein Pcdhac2
KeywordsCELL ADHESION
Function / homology
Function and homology information


serotonergic neuron axon guidance / homophilic cell-cell adhesion / calcium ion binding / 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 alpha C2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Shapiro, L.
CitationJournal: Cell / Year: 2015
Title: Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions.
Authors: Rubinstein, R. / Thu, C.A. / Goodman, K.M. / Wolcott, H.N. / Bahna, F. / Mannepalli, S. / Ahlsen, G. / Chevee, M. / Halim, A. / Clausen, H. / Maniatis, T. / Shapiro, L. / Honig, B.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jul 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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 Pcdhac2
B: Protein Pcdhac2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,64919
Polymers72,2262
Non-polymers1,42317
Water72140
1
A: Protein Pcdhac2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,93510
Polymers36,1131
Non-polymers8229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein Pcdhac2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7149
Polymers36,1131
Non-polymers6018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.990, 97.130, 147.680
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein Pcdhac2 / Protocadherin alpha C2


Mass: 36113.094 Da / Num. of mol.: 2 / Fragment: UNP residues 42-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhac2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91Y09
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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
#3: 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


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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 28% PEG MME 500, 100mM sodium acetate, pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→31.62 Å / Num. obs: 26357 / % possible obs: 95.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPO

4zpo


Resolution: 2.4→31.62 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1313 4.98 %
Rwork0.2076 --
obs0.2099 26357 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 70 40 4855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034894
X-RAY DIFFRACTIONf_angle_d0.736683
X-RAY DIFFRACTIONf_dihedral_angle_d12.1511823
X-RAY DIFFRACTIONf_chiral_restr0.027794
X-RAY DIFFRACTIONf_plane_restr0.003888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.33651490.30242768X-RAY DIFFRACTION93
2.4962-2.60980.33261280.28272650X-RAY DIFFRACTION94
2.6098-2.74730.35561460.29272798X-RAY DIFFRACTION95
2.7473-2.91930.34421380.28082725X-RAY DIFFRACTION96
2.9193-3.14450.30841560.27152836X-RAY DIFFRACTION96
3.1445-3.46060.27931340.22172773X-RAY DIFFRACTION96
3.4606-3.96050.26711540.20062774X-RAY DIFFRACTION96
3.9605-4.98670.19891550.15862874X-RAY DIFFRACTION97
4.9867-31.62440.17931530.15492846X-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)
13.0611-1.05381.44158.0314-7.37218.3902-0.0279-0.16460.0215-0.37980.20770.00110.058-0.1324-0.15340.4770.0101-0.02250.3199-0.02710.316452.9486-24.0463.7016
21.15150.986-0.15825.9724-2.2654.8158-0.01810.02750.14520.30420.0924-0.1349-0.255-0.3083-0.07460.15210.0080.0150.29670.04220.3770.729-71.748458.8638
31.6692-1.52050.25729.6994-3.07121.7760.1880.137-0.008-0.3515-0.0637-0.12710.34030.1562-0.10360.26590.03640.01140.3179-0.00650.335654.761412.882642.1799
43.2375-4.42491.91626.9256-2.83161.9255-0.1968-0.04870.26380.0407-0.0703-0.2518-0.73780.08240.21560.75570.161-0.02530.40980.0760.479662.304-33.660641.7408
50.4315-0.03790.44525.027-5.2788.0134-0.05850.19830.26190.29570.09950.1476-0.88040.3394-0.02230.6682-0.03510.02930.5950.19930.514146.684354.860815.2854
62.2589-1.0905-0.20694.3058-3.53576.02840.34050.2950.0542-0.2232-0.16420.09430.09710.0823-0.14590.68410.1429-0.14080.4412-0.0230.495543.95698.396321.0369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and ((resseq 1:98)))
2X-RAY DIFFRACTION2(chain 'B' and ((resseq 1:98)))
3X-RAY DIFFRACTION3(chain 'A' and ((resseq 99:206)))
4X-RAY DIFFRACTION4(chain 'B' and ((resseq 99:206)))
5X-RAY DIFFRACTION5(chain 'A' and ((resseq 207:317)))
6X-RAY DIFFRACTION6(chain 'B' and ((resseq 207:317)))

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