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- PDB-1z9m: Crystal Structure of Nectin-like molecule-1 protein Domain 1 -

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Basic information

Entry
Database: PDB / ID: 1z9m
TitleCrystal Structure of Nectin-like molecule-1 protein Domain 1
ComponentsGAPA225
KeywordsCELL ADHESION / Nectin-like / Ig-like domain / V domain
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / Adherens junctions interactions / adherens junction organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell-cell junction / membrane => GO:0016020 / protein homodimerization activity / plasma membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cell adhesion molecule 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsDong, X. / Xu, F. / Gong, Y. / Gao, J. / Lin, P. / Chen, T. / Peng, Y. / Qiang, B. / Yuan, J. / Peng, X. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the V Domain of Human Nectin-like Molecule-1/Syncam3/Tsll1/Igsf4b, a Neural Tissue-specific Immunoglobulin-like Cell-Cell Adhesion Molecule
Authors: Dong, X. / Xu, F. / Gong, Y. / Gao, J. / Lin, P. / Chen, T. / Peng, Y. / Qiang, B. / Yuan, J. / Peng, X. / Rao, Z.
History
DepositionApr 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAPA225
B: GAPA225


Theoretical massNumber of molelcules
Total (without water)31,7372
Polymers31,7372
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 77.500, 102.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GAPA225 / Nectin-like molecule_1 Domain 1


Mass: 15868.651 Da / Num. of mol.: 2 / Fragment: residues 37-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 37181789, UniProt: Q8N126*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.4 Å3/Da / Density % sol: 48.5 % / Description: the file contains Friedel pairs.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium Formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9000, 0.9788, 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 10, 2005
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97881
30.97931
ReflectionResolution: 2.4→50 Å / Num. all: 24704 / Num. obs: 24704 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→48.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs.
RfactorNum. reflectionSelection details
Rfree0.274 2138 Random
Rwork0.227 --
all0.244 23158 -
obs0.244 23089 -
Refinement stepCycle: LAST / Resolution: 2.4→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 196 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0095
X-RAY DIFFRACTIONc_angle_deg1.6

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