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- PDB-3bop: Structure of mouse beta-neurexin 2D4 -

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Basic information

Entry
Database: PDB / ID: 3bop
TitleStructure of mouse beta-neurexin 2D4
Componentsbeta-Neurexin 2D4
KeywordsCELL ADHESION / beta-Neurexin 2D4 / LNS6 / Lectin
Function / homology
Function and homology information


Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
LAM_G_DOMAIN domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsKoehnke, J. / Jin, X. / Shapiro, L.
CitationJournal: Structure / Year: 2008
Title: Crystal Structures of beta-Neurexin 1 and beta-Neurexin 2 Ectodomains and Dynamics of Splice Insertion Sequence 4.
Authors: Koehnke, J. / Jin, X. / Trbovic, N. / Katsamba, P.S. / Brasch, J. / Ahlsen, G. / Scheiffele, P. / Honig, B. / Palmer, A.G. / Shapiro, L.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-Neurexin 2D4
B: beta-Neurexin 2D4
C: beta-Neurexin 2D4


Theoretical massNumber of molelcules
Total (without water)57,1183
Polymers57,1183
Non-polymers00
Water2,486138
1
A: beta-Neurexin 2D4


Theoretical massNumber of molelcules
Total (without water)19,0391
Polymers19,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: beta-Neurexin 2D4


Theoretical massNumber of molelcules
Total (without water)19,0391
Polymers19,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: beta-Neurexin 2D4


Theoretical massNumber of molelcules
Total (without water)19,0391
Polymers19,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.485, 96.983, 62.584
Angle α, β, γ (deg.)90.000, 105.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-Neurexin 2D4


Mass: 19039.270 Da / Num. of mol.: 3 / Fragment: LNS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrxn2 / Plasmid: pGEX-NRX2D4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3TQ54
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 4000, 0.2M (NH4)2SO4, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2006 / Details: Si111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 10939 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Num. unique all: 1116 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 3→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.863 / SU B: 42.254 / SU ML: 0.429 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 546 5 %RANDOM
Rwork0.211 ---
obs0.215 10871 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å21.82 Å2
2---2.58 Å20 Å2
3---3.81 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 0 138 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223950
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9455372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51423.209187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3471536
X-RAY DIFFRACTIONr_chiral_restr0.0670.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023080
X-RAY DIFFRACTIONr_nbd_refined0.1910.21597
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.25
X-RAY DIFFRACTIONr_mcbond_it0.171.52535
X-RAY DIFFRACTIONr_mcangle_it0.31123999
X-RAY DIFFRACTIONr_scbond_it0.35931585
X-RAY DIFFRACTIONr_scangle_it0.6174.51373
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 33 -
Rwork0.278 768 -
all-801 -
obs--98.4 %
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)
13.1561-0.32061.02794.967-2.1173.91430.0637-0.11750.29730.3988-0.0736-0.0863-0.50160.10510.00990.0132-0.05690.0031-0.0743-0.03-0.069717.527-0.494619.4016
26.71680.999-1.40751.9075-0.04221.7085-0.00860.1799-0.1197-0.1396-0.0646-0.0430.19440.07660.07320.0007-0.02120.0395-0.014-0.0636-0.107922.32817.98435.3627
32.9469-1.38730.75337.917-4.43515.8795-0.0308-0.0914-0.06960.13880.20710.86430.1243-0.3661-0.1763-0.1049-0.01890.0485-0.00950.0080.077313.382124.3779-4.6493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA86 - 2601 - 175
2X-RAY DIFFRACTION2BB87 - 2602 - 175
3X-RAY DIFFRACTION3CC86 - 2601 - 175

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