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- PDB-1cs6: N-TERMINAL FRAGMENT OF AXONIN-1 FROM CHICKEN -

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Basic information

Entry
Database: PDB / ID: 1cs6
TitleN-TERMINAL FRAGMENT OF AXONIN-1 FROM CHICKEN
ComponentsAXONIN-1
KeywordsCELL ADHESION / NEURAL CELL ADHESION
Function / homology
Function and homology information


presynaptic membrane organization / cell-cell adhesion mediator activity / neuron cell-cell adhesion / side of membrane / cell adhesion molecule binding / axon guidance / cell-cell adhesion / brain development / axon / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsFreigang, J. / Proba, K. / Diederichs, K. / Sonderegger, P. / Welte, W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: The crystal structure of the ligand binding module of axonin-1/TAG-1 suggests a zipper mechanism for neural cell adhesion.
Authors: Freigang, J. / Proba, K. / Leder, L. / Diederichs, K. / Sonderegger, P. / Welte, W.
History
DepositionAug 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AXONIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6952
Polymers42,6031
Non-polymers921
Water6,431357
1
A: AXONIN-1
hetero molecules

A: AXONIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3904
Polymers85,2052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Unit cell
Length a, b, c (Å)60.583, 45.540, 99.548
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is an oligomer generated by the two-fold screw axis.

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Components

#1: Protein AXONIN-1


Mass: 42602.734 Da / Num. of mol.: 1 / Fragment: IG1-4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PTFT / Production host: Escherichia coli (E. coli) / References: UniProt: P28685
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 10000, sodium formiate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
225 mMTris-HCl1drop
3125 mM1dropNaCl
415-17 %(w/v)PEG100001reservoir
5150 mMsodium formiate1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 50527 / Num. obs: 48051 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.206 / Num. unique all: 3896 / % possible all: 83.3
Reflection shell
*PLUS
% possible obs: 83.3 % / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SHARPphasing
CNS0.4refinement
XDSdata scaling
RefinementResolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 566597.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2384 5 %RANDOM
Rwork0.226 ---
all0.226 50456 --
obs0.226 47550 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.17 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--5.22 Å20 Å2-6.62 Å2
2--2.27 Å20 Å2
3---2.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 6 357 3362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.282
X-RAY DIFFRACTIONc_scangle_it2.052.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 333 4.7 %
Rwork0.265 6769 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3GOL.PAR
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.265

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