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- PDB-3qcw: Structure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts -

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Basic information

Entry
Database: PDB / ID: 3qcw
TitleStructure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts
ComponentsNeurexin-1-alpha
KeywordsCELL ADHESION / synaptic adhesion molecule
Function / homologyConcanavalin A-like lectin/glucanase domain superfamily / Aspartic acid and asparagine hydroxylation site. / EGF-like domain profile. / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Laminin G domain / Neurexin/syndecan/glycophorin C / Laminin G domain profile. / Syndecan/Neurexin domain / Neurexin ...Concanavalin A-like lectin/glucanase domain superfamily / Aspartic acid and asparagine hydroxylation site. / EGF-like domain profile. / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Laminin G domain / Neurexin/syndecan/glycophorin C / Laminin G domain profile. / Syndecan/Neurexin domain / Neurexin / EGF-like domain / Syndecan domain / Laminin G domain / neuroligin family protein binding / presynaptic membrane / cell junction / cell adhesion / integral component of membrane / metal ion binding / Neurexin-1
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / 2.65 Å resolution
AuthorsRudenko, G.
CitationJournal: Structure / Year: 2011
Title: The Structure of Neurexin 1 alpha Reveals Features Promoting a Role as Synaptic Organizer
Authors: Chen, F. / Venugopal, V. / Murray, B. / Rudenko, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 17, 2011 / Release: Jun 15, 2011
RevisionDateData content typeGroupCategoryProviderType
1.0Jun 15, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 26, 2017Structure modelRefinement description / Source and taxonomyentity_src_gen / software
1.3Nov 8, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurexin-1-alpha
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,8346
Polyers274,9492
Non-polymers8854
Water0
1
A: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9173
Polyers137,4751
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9173
Polyers137,4751
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.953, 114.543, 159.581
Angle α, β, γ (deg.)90.610, 90.870, 92.180
Int Tables number1
Space group name H-MP 1

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Components

#1: Protein/peptide Neurexin-1-alpha


Mass: 137474.641 Da / Num. of mol.: 2 / Fragment: UNP residues 31-1355 / Mutation: N190Q, SEE REMARK 999 / Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q28146
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
Sequence detailsPROTEIN CONSTRUCT IS A SPLICE FORM THAT DOES NOT CONTAIN SPLICE INSERTS AT SITES SS1 ...PROTEIN CONSTRUCT IS A SPLICE FORM THAT DOES NOT CONTAIN SPLICE INSERTS AT SITES SS1 [DEL(258-277)], SS2 [DEL(378-393)], SS3 [DEL(790-799),D790G], AND SS4 [DEL(1248-1278)]. Q612E AND I1112F ARE NATURAL ISOFORMS.

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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: 4.05 / Density percent sol: 69.62 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop
Details: 5-10% PEG8000 or PEG10000, 2.5 mM calcium chloride, 100 mM bicine, pH 8.0-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 21-ID-D / Synchrotron site: APS / Beamline: 21-ID-D / Wavelength: 1.1272
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Jun 12, 2010
RadiationMonochromator: Kohzu / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionAv sigmaI over netI: 17.83 / Number: 267276 / Rmerge I obs: 0.135 / Chi squared: 1.9 / Highest resolution: 3.25 Å / Lowest resolution: 5 Å / Number obs: 67601 / Percent possible obs: 98.6 / Redundancy: 4 %
Diffraction reflection shell

Id: 1

Highest resolutionLowest resolutionRmerge I obsChi squaredPercent possible obsRedundancy
8.8150.000.0354.01496.203.90
7.008.810.0512.78998.304.00
6.117.000.0742.31398.804.00
5.566.110.0831.99598.704.00
5.165.560.0882.15898.704.00
4.855.160.0942.04799.004.00
4.614.850.0912.00899.004.00
4.414.610.1071.96098.604.00
4.244.410.1301.82499.204.00
4.094.240.1741.71598.704.00
3.974.090.1821.68599.204.00
3.853.970.2181.58298.804.00
3.753.850.2601.57999.104.00
3.663.750.3071.52998.804.00
3.583.660.3601.55498.904.00
3.503.580.3881.51198.704.00
3.433.500.4871.47498.803.90
3.373.430.5581.43898.903.90
3.313.370.6341.39498.403.80
3.253.310.8021.45397.903.70
ReflectionD resolution high: 2.65 Å / D resolution low: 5 Å / Number obs: 124701 / Rmerge I obs: 0.079 / Chi squared: 1.591 / NetI over sigmaI: 14.5 / Redundancy: 3.4 % / Percent possible obs: 98.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.5262.6502.70062061.2393.20098.200
0.4502.7002.74061691.2033.30097.700
0.4242.7402.80061871.3063.30097.300
0.3802.8002.85062111.3313.30098.400
0.3212.8502.92061911.3303.30096.900
0.2522.9202.98062221.3903.30099.200
0.2152.9803.06062001.4793.40097.000
0.1823.0603.14062401.5753.40099.400
0.1463.1403.23061871.4413.40097.500
0.1303.2303.34062511.5443.40099.300
0.1113.3403.46062261.6873.40098.300
0.0923.4603.60062911.7503.40098.000
0.0823.6003.76062041.8143.40099.600
0.0763.7603.96062781.9303.40098.800
0.0663.9604.21062311.9583.40098.700
0.0604.2104.53062911.9543.40099.100
0.0534.5304.99063121.9483.40099.100
0.0524.9905.71062671.8223.40099.100
0.0485.7107.19062981.6153.40099.500
0.0367.19050.00062391.3983.30098.600

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
DENZOdata reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
PHASERphasingRandy J. Readcimr-phaser[at]lists.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk/phaser/program
REFMACrefinementGarib N. Murshudovgarib[at]ysbl.york.ac.ukhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramFortran_77
PDB_EXTRACT3.10data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++June 10, 2010
HKL-2000data collection
RefineMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Correlation coeff Fo to Fc: 0.936 / Correlation coeff Fo to Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / Overall FOM work R set: 0.8568 / Overall SU B: 16.733 / Overall SU ML: 0.161 / Overall SU R Cruickshank DPI: 0.3693 / Overall SU R free: 0.2628 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.299 / Overall ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: BABINET MODEL WITH MASK
Displacement parametersB iso max: 200.33 Å2 / B iso mean: 65.5416 Å2 / B iso min: 2.83 Å2 / Aniso B11: -3.76 Å2 / Aniso B12: -1.23 Å2 / Aniso B13: 0.31 Å2 / Aniso B22: 0.45 Å2 / Aniso B23: 0.16 Å2 / Aniso B33: 3.23 Å2
Least-squares processR factor R free: 0.2296 / R factor R work: 0.2082 / R factor obs: 0.2093 / Highest resolution: 2.65 Å / Lowest resolution: 3 Å / Number reflection R free: 6451 / Number reflection obs: 116726 / Percent reflection R free: 5.2 / Percent reflection obs: 98.43 / WR factor R free: 0.2745 / WR factor R work: 0.2672
Refine hist #LASTHighest resolution: 2.65 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 15384 / Nucleic acid: 0 / Ligand: 56 / Solvent: 0 / Total: 15440
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215772
X-RAY DIFFRACTIONr_angle_refined_deg1.7301.95521400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8945.0002004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06524.520708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21815.0002590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.47415.00084
X-RAY DIFFRACTIONr_chiral_restr0.1070.2002398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02011978
X-RAY DIFFRACTIONr_nbd_refined0.2320.2006371
X-RAY DIFFRACTIONr_nbtor_refined0.3210.20010789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.200539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.20088
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.20016
X-RAY DIFFRACTIONr_mcbond_it0.7431.50010119
X-RAY DIFFRACTIONr_mcangle_it1.2222.00015916
X-RAY DIFFRACTIONr_scbond_it2.1813.0006339
X-RAY DIFFRACTIONr_scangle_it3.3174.5005484
Refine LS restraints ncs

Dom ID: 1 / Auth asym ID: A / Refine ID: X-RAY DIFFRACTION

Ens IDNumberTypeRms dev positionWeight position
11409TIGHT POSITIONAL0.0200.050
11409TIGHT THERMAL0.0300.500
21510TIGHT POSITIONAL0.0300.050
21510TIGHT THERMAL0.0500.500
3330TIGHT POSITIONAL0.0300.050
3330TIGHT THERMAL0.0700.500
41408TIGHT POSITIONAL0.0400.050
41408TIGHT THERMAL0.1200.500
51374TIGHT POSITIONAL0.0400.050
51374TIGHT THERMAL0.1300.500
6305TIGHT POSITIONAL0.0300.050
6305TIGHT THERMAL0.0800.500
71384TIGHT POSITIONAL0.0300.050
71384TIGHT THERMAL0.0800.500
Refine LS shellHighest resolution: 2.65 Å / R factor R free: 0.331 / R factor R work: 0.307 / Lowest resolution: 2.718 Å / Number reflection R free: 491 / Number reflection R work: 8443 / Number reflection all: 8934 / Total number of bins used: 20 / Percent reflection obs: 97.78
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
17.59444.32072.18628.35752.95824.87900.05320.02820.7198-0.3264-0.56540.1641-0.86360.05610.51220.6984-0.0409-0.05731.15560.1854-0.07241.4872127.147619.2269
21.39860.1905-0.18580.96050.05393.9436-0.07790.98540.1288-0.59230.0588-0.0044-0.37820.00620.0192-0.0254-0.0546-0.02140.22400.0238-0.30806.0110119.484066.0445
34.1354-0.2070-0.38362.9049-0.47641.4697-0.00380.0500-0.4686-0.00330.02710.25100.1491-0.1926-0.0234-0.43030.0046-0.0027-0.45790.0244-0.32089.780499.9776108.0571
43.2210-1.03890.83265.5214-0.01742.2056-0.0720-0.13800.75630.19370.10670.0952-0.69390.0447-0.03470.0168-0.04830.0780-0.4046-0.06360.2560-10.8344154.7958110.5526
59.4967-4.3123-1.76197.69332.55266.0080-0.1349-0.1427-0.87760.3539-0.31390.14661.07880.11890.44880.73470.04340.02611.02540.1826-0.071333.6869-16.0905190.7150
61.5480-0.18110.13481.02260.20743.9861-0.0724-1.0100-0.12430.62000.0765-0.04080.42850.0299-0.0041-0.02560.0661-0.01000.18670.0280-0.306739.8600-8.7111143.7160
74.37400.21270.44113.0854-0.73731.3693-0.00100.01340.4532-0.01480.05980.2680-0.1723-0.1965-0.0588-0.4202-0.01070.0019-0.45050.0323-0.309644.673810.5807101.6104
84.96972.6663-1.38295.4781-0.25412.6133-0.27040.1234-1.1714-0.28770.1526-0.37910.81150.13260.11780.06190.06910.0184-0.3710-0.07970.365123.8057-44.301599.0140
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS ID
1A281A4851
2A486A9092
3A910A10873
4A1088A13374
5B281B4855
6B486B9096
7B910B10877
8B1088B13378

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