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- PDB-6cw1: Crystal structure of Neurexin-1 alpha ectodomain fragment, L2-L3 -

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Basic information

Entry
Database: PDB / ID: 6cw1
TitleCrystal structure of Neurexin-1 alpha ectodomain fragment, L2-L3
ComponentsNeurexin-1
KeywordsCELL ADHESION / LNS domain / Beta-Sandwich / Synapse
Function / homology
Function and homology information


neuroligin family protein binding / cell projection / presynaptic membrane / cell adhesion / cell junction / integral component of membrane / metal ion binding
EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Laminin G domain / Neurexin/syndecan/glycophorin C / Concanavalin A-like lectin/glucanase domain superfamily / Syndecan/Neurexin domain / Laminin G domain
Neurexin-1
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsMisra, A. / Rudenko, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurexin-1
B: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)89,0342
Polymers89,0342
Non-polymers00
Water21612
1
A: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polymers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1


Theoretical massNumber of molelcules
Total (without water)44,5171
Polymers44,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)87.144, 62.901, 113.061
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Refine code: 0 / Auth seq-ID: 279 - 672

Dom-IDAuth asym-ID
1A
2B

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Components

#1: Protein/peptide Neurexin-1 / / Neurexin I-alpha / Neurexin-1-alpha


Mass: 44517.121 Da / Num. of mol.: 2 / Fragment: Alpha fragment L2-L3, residues 258-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid: pGEX-KG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q28146
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.45 Å3/Da / Density % sol: 64.39 % / Mosaicity: 1.742 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.9 M NaCITRATE, 0.1 M TRIS PH 8.0, 5 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.10208 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10208 Å / Relative weight: 1
ReflectionResolution: 2.84→50.01 Å / Num. obs: 28540 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Χ2: 1.469 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.84-2.952.40.522.225550.7150.3910.6541.17889.1
2.95-3.072.70.39127740.7960.2930.4921.39296.4
3.07-3.212.90.27528220.9020.1930.3381.32598.8
3.21-3.383.30.17428960.9660.1130.2081.41899.9
3.38-3.593.70.1328790.9840.0790.1531.49199.9
3.59-3.873.70.10528760.9890.0640.1231.66199.9
3.87-4.263.80.08228930.9910.050.0961.502100
4.26-4.873.70.06729200.9910.0410.0791.455100
4.87-6.143.70.06329290.9920.0380.0741.519100
6.14-50.013.60.06229960.9940.0370.0731.50799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QCW
Resolution: 2.84→50.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 35.561 / SU ML: 0.307 / SU R Cruickshank DPI: 0.7583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.758 / ESU R Free: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1418 5 %RANDOM
Rwork0.2216 ---
Obs0.2233 27112 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.21 Å2 / Biso mean: 52.259 Å2 / Biso min: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.39 Å2
2---0.57 Å2-0 Å2
3---2.3 Å2
Refinement stepCycle: final / Resolution: 2.84→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 0 12 5742
Biso mean---42.12 -
Num. residues----762
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0130.0195857
r_bond_other_d0.0010.025216
r_angle_refined_deg1.5081.9567970
r_angle_other_deg0.809312073
r_dihedral_angle_1_deg7.35758
r_dihedral_angle_2_deg35.36224.733243
r_dihedral_angle_3_deg18.42615900
r_dihedral_angle_4_deg17.0541519
r_chiral_restr0.090.2910
r_gen_planes_refined0.0080.0216635
r_gen_planes_other0.0020.021180
Refine LS restraints NCS

Ens-ID: 1 / Number: 22294 / Refinement-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.837→2.911 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 75 -
Rwork0.312 1668 -
All-1743 -
Obs--82.1 %
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.2153-1.07643.52333.3341-1.38294.9136-0.132-0.225-0.2281-0.3245-0.0278-0.13780.1433-0.0850.15970.1970.0528-0.07470.037-0.01320.153160.9817-2.572731.2217
20.7574-0.88711.18463.835-2.5325.4667-0.16140.09610.09480.0734-0.1277-0.2364-0.27780.39690.28910.4021-0.0009-0.22380.12250.03930.218948.02220.03671.9804
36.6581-0.91142.62952.5006-0.77622.4597-0.1664-0.33120.5166-0.11630.0072-0.209-0.4035-0.32150.15920.15540.0462-0.09090.0945-0.00550.314588.62050.21650.624
46.4086-2.0189-0.97773.8886-0.04340.72650.08620.4989-0.3071-0.1683-0.08240.25230.0915-0.0866-0.00390.08770.0043-0.09080.0421-0.00680.2485120.6521-22.476852.1975
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-ID
11A279 - 485
22A486 - 673
33B278 - 485
44B486 - 674

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