PDB-2h0b: Crystal Structure of the second LNS/LG domain from Neurexin 1 alpha

ID or keywords:

Entry

Database: PDB / ID: 2h0b

Title

Crystal Structure of the second LNS/LG domain from Neurexin 1 alpha

Components

Neurexin-1-alpha

Keywords

CELL ADHESION / b-sandwich

Function / homology

Function and homology information

neuroligin family protein binding / cell projection / presynaptic membrane / cell adhesion / metal ion binding
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Sheckler, L.R. / Henry, L. / Sugita, S. / Sudhof, T.C. / Rudenko, G.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Second LNS/LG Domain from Neurexin 1{alpha}: Ca2+ binding and the effects of alternative splicing
Authors: Sheckler, L.R. / Henry, L. / Sugita, S. / Sudhof, T.C. / Rudenko, G.

History

Deposition	May 14, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Remark 999

SEQUENCE The sequence corresponds to isoform 9 of UNP entry NRX1A_BOVIN.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2h0b.cif.gz	159 KB	Display	PDBx/mmCIF format
PDB format	pdb2h0b.ent.gz	130 KB	Display	PDB format
PDBx/mmJSON format	2h0b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2h0b_validation.pdf.gz	467.2 KB	Display	wwPDB validaton report
Full document	2h0b_full_validation.pdf.gz	479 KB	Display
Data in XML	2h0b_validation.xml.gz	33.1 KB	Display
Data in CIF	2h0b_validation.cif.gz	46.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0b ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0b	HTTPS FTP

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Related structure data

Similar structure data	5glx-d 2jnp-d 2w7u-2 3s8j-1 5b5s-d 2i2s-2 2ayk-d 2w7u-3 2w7u-4 5a0d-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (3) #126 - Jun 2010 Epidermal Growth Factor similarity (4) #75 - Mar 2006 Tissue Factor similarity (4) #17 - May 2001 Cyclooxygenase similarity (1)

Deposited unit

A: Neurexin-1-alpha

B: Neurexin-1-alpha

C: Neurexin-1-alpha

D: Neurexin-1-alpha

hetero molecules

81.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Neurexin-1-alpha

hetero molecules

defined by author
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Neurexin-1-alpha

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Neurexin-1-alpha

hetero molecules

defined by author
20.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Neurexin-1-alpha

hetero molecules

defined by author
20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.032, 61.586, 66.640
Angle α, β, γ (deg.)	78.47, 78.74, 84.68
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	A
6	1	B
7	1	C
8	1	D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	PRO	A	A	280 - 357	4 - 81
2	1	GLU	PRO	B	B	280 - 357	4 - 81
3	1	GLU	PRO	C	C	280 - 357	4 - 81
4	1	GLU	PRO	D	D	280 - 357	4 - 81
5	2	GLY	HIS	A	A	360 - 473	84 - 182
6	2	GLY	HIS	B	B	360 - 473	84 - 182
7	2	GLY	HIS	C	C	360 - 473	84 - 182
8	2	GLY	HIS	D	D	360 - 473	84 - 182

#1: Protein	Neurexin-1-alpha / Neurexin I-alpha Mass: 20353.170 Da / Num. of mol.: 4 / Fragment: second LNS/LG domain (residues 295-476) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q28146
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.74 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% P8000, 0.1M Tris, 5mM CaCl2, 1% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: F2 / Wavelength: 0.978952, 0.979338, 0.980111

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2005

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.978952	1
2	0.979338	1
3	0.980111	1

Reflection

D res high: 2.1 Å / D res low: 40 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
3.7	1	10.9	190980	0.089	1.5	52304	98.1
3.7	2	12.2	191448	0.09	1.55	52276	98.2
3.6	3	11.3	187261	0.072	0.96	51547	96.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.52	40	99.5	1	0.063	3.671	3.8
3.59	4.52	99.1	1	0.059	1.79	3.9
3.14	3.59	98.8	1	0.075	1.592	3.9
2.85	3.14	98.5	1	0.098	1.5	3.9
2.65	2.85	98.2	1	0.134	1.381	3.8
2.49	2.65	98	1	0.179	1.113	3.7
2.37	2.49	97.6	1	0.213	0.955	3.6
2.26	2.37	97.6	1	0.26	0.811	3.6
2.18	2.26	97.3	1	0.305	0.958	3.4
2.1	2.18	96.6	1	0.324	0.714	2.9
4.52	40	99.5	2	0.056	2.235	3.9
3.59	4.52	99.1	2	0.07	2.201	3.9
3.14	3.59	98.8	2	0.087	2.061	3.9
2.85	3.14	98.5	2	0.101	1.774	3.9
2.65	2.85	98.2	2	0.13	1.671	3.8
2.49	2.65	98	2	0.166	1.253	3.7
2.37	2.49	97.7	2	0.194	1.037	3.6
2.26	2.37	97.6	2	0.235	0.89	3.6
2.18	2.26	97.3	2	0.276	1.163	3.4
2.1	2.18	96.9	2	0.291	0.778	2.9
4.52	40	99.5	3	0.039	1	3.9
3.59	4.52	99.1	3	0.047	1.005	3.9
3.14	3.59	98.8	3	0.065	1.07	3.9
2.85	3.14	98.5	3	0.088	1.072	3.9
2.65	2.85	98.2	3	0.13	1.097	3.8
2.49	2.65	98	3	0.176	0.928	3.7
2.37	2.49	97.6	3	0.213	0.833	3.6
2.26	2.37	97.3	3	0.24	0.759	3.5
2.18	2.26	93	3	0.257	0.968	3.2
2.1	2.18	85.9	3	0.265	0.771	2.7

Reflection

Resolution: 2.1→40 Å / Num. obs: 51547 / % possible obs: 96.6 % / Redundancy: 3.6 % / R_merge(I) obs: 0.072 / Χ²: 0.964 / Net I/σ(I): 11.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.18	2.7	0.265	4563	0.771	1	85.9
2.18-2.26	3.2	0.257	4969	0.968	1	93
2.26-2.37	3.5	0.24	5250	0.759	1	97.3
2.37-2.49	3.6	0.213	5173	0.833	1	97.6
2.49-2.65	3.7	0.176	5231	0.928	1	98
2.65-2.85	3.8	0.13	5245	1.097	1	98.2
2.85-3.14	3.9	0.088	5249	1.072	1	98.5
3.14-3.59	3.9	0.065	5267	1.07	1	98.8
3.59-4.52	3.9	0.047	5291	1.005	1	99.1
4.52-40	3.9	0.039	5309	1	1	99.5

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Phasing

Phasing

Method:

MAD

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	40.976	0.988	0.001	0.013	0.66
2	Se	26.405	0.569	0.346	0.513	0.677
3	Se	60	0.725	0.56	0.453	0.781
4	Se	41.338	0.265	0.298	0.072	0.618
5	Se	39.15	0.384	0.656	0.287	0.8
6	Se	23.181	0.823	0.968	0.891	0.683
7	Se	39.915	0.971	0.091	0.275	0.729
8	Se	43.872	0.423	0.515	0.015	0.827
9	Se	41.208	0.988	0.85	0.541	0.645
10	Se	30.775	0.151	0.887	0.348	0.519
11	Se	36.817	0.63	0.32	0.698	0.539
12	Se	32.239	0.345	0.53	0.218	0.484
13	Se	38.689	0.001	0.761	0.832	0.467
14	Se	25.012	0.603	0.209	0.832	0.407
15	Se	58.326	0.164	0.966	0.963	0.65
16	Se	57.783	0.811	0.88	0.541	0.519

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 22156

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.13-100	56.6	0.905	512
7.51-9.13	52.8	0.911	501
6.65-7.51	60	0.896	516
6.09-6.65	63.3	0.891	503
5.65-6.09	60.7	0.894	556
5.3-5.65	52.7	0.897	596
5-5.3	60.1	0.898	601
4.75-5	53.3	0.914	660
4.53-4.75	52.2	0.909	700
4.34-4.53	57.5	0.882	720
4.18-4.34	54.4	0.881	755
4.03-4.18	68.8	0.848	774
3.89-4.03	65.7	0.812	794
3.77-3.89	65.6	0.832	847
3.66-3.77	66	0.833	859
3.56-3.66	64.4	0.829	877
3.46-3.56	71.6	0.815	915
3.38-3.46	73.5	0.799	932
3.3-3.38	68.4	0.787	955
3.22-3.3	70.9	0.76	963
3.15-3.22	72.1	0.747	997
3.08-3.15	70.4	0.749	1033
3.02-3.08	75.5	0.735	1045
2.96-3.02	77.2	0.712	1072
2.91-2.96	76.2	0.692	1066
2.86-2.91	80.4	0.639	1103
2.8-2.86	77.4	0.599	1304

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.05	phasing
DM		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 2.1→20 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.935 / SU B: 10.098 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The authors state that the following water molecules have shown varying quality of electron density as refinement of the model progressed and are therefore considered not reliably known: HOH ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.233	2577	5 %	RANDOM
R_work	0.184	-	-	-
all	0.186	-	-	-
obs	0.18607	51492	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 36.373 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.21 Å²	3.82 Å²	-0.68 Å²
2-	-	0.15 Å²	-0.71 Å²
3-	-	-	-1.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5553	0	28	444	6025

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5672
X-RAY DIFFRACTION	r_angle_refined_deg	1.391	1.95	7674
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.085	5	719
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.836	25.333	255
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.908	15	933
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.045	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	863
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4289
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	2330
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	3763
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	457
X-RAY DIFFRACTION	r_metal_ion_refined	0.133	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.229	0.2	58
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.253	0.2	34
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.068	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.741	1.5	3666
X-RAY DIFFRACTION	r_mcangle_it	1.042	2	5749
X-RAY DIFFRACTION	r_scbond_it	2.014	3	2250
X-RAY DIFFRACTION	r_scangle_it	3.005	4.5	1925

Refine LS restraints NCS

Ens-ID: 1 / Number: 1303 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	LOOSE POSITIONAL	0.4	5
2	B	LOOSE POSITIONAL	0.4	5
3	C	LOOSE POSITIONAL	0.44	5
4	D	LOOSE POSITIONAL	0.39	5
1	A	LOOSE THERMAL	1.63	10
2	B	LOOSE THERMAL	1.58	10
3	C	LOOSE THERMAL	1.66	10
4	D	LOOSE THERMAL	1.73	10

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	158	-
R_work	0.248	3087	-
obs	-	3245	100 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.1744	-1.0625	0.7758	2.4769	-0.1437	4.0717	0.2082	0.0648	-0.1702	-0.0255	-0.0969	0.0233	0.2985	0.0552	-0.1113	-0.1882	-0.0572	0.0182	-0.1876	0.0145	-0.1438	1.2632	5.3942	51.5698
2	2.2995	-0.7619	0.1012	2.8266	0.7323	3.4326	-0.092	-0.1057	0.0822	0.0479	0.0888	-0.0796	-0.1219	-0.0139	0.0032	-0.2272	-0.0564	0.0114	-0.1826	0.0242	-0.1577	9.8688	-1.5674	16.5624
3	3.7993	-3.0095	0.7416	4.5808	-0.3568	2.8048	0.0913	0.1279	0.1074	-0.2031	-0.1212	-0.2079	-0.021	0.3101	0.0299	-0.0958	0.0003	-0.0017	-0.0505	-0.0033	-0.1663	41.3158	32.8735	29.8594
4	3.6221	-2.8025	-0.2295	4.7081	0.3913	1.7215	0.165	0.0225	0.2444	-0.2322	-0.2018	-0.2105	0.0462	-0.1629	0.0369	-0.101	-0.0602	0.033	-0.1507	0.0038	-0.1135	28.6061	25.2002	-0.4187

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	280 - 475	4 - 184
2	2	B	B	280 - 475	4 - 184
3	3	C	C	278 - 475	2 - 184
4	4	D	D	279 - 475	3 - 184

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+
Jul 12, 2017. Major update of PDB

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Yorodumi