PDB-7y5j: Crystal structure of sDscam Ig1 domain, isoform alpha1v7

ID or keywords:

Entry

Database: PDB / ID: 7y5j

Title

Crystal structure of sDscam Ig1 domain, isoform alpha1v7

Components

Down Syndrome Cell Adhesion Molecules

Keywords

CELL ADHESION / cell surface receptor

Biological species

Chelicerata (chelicerates)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Chen, Q. / Yu, Y. / Cheng, J.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Structural basis for the self-recognition of sDSCAM in Chelicerata.
Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q.

History

Deposition	Jun 17, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 24, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7y5j.cif.gz	73.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7y5j.ent.gz	53.3 KB	Display	PDB format
PDBx/mmJSON format	7y5j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7y5j_validation.pdf.gz	412.3 KB	Display	wwPDB validaton report
Full document	7y5j_full_validation.pdf.gz	413 KB	Display
Data in XML	7y5j_validation.xml.gz	7.6 KB	Display
Data in CIF	7y5j_validation.cif.gz	10.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/7y5j ftp://data.pdbj.org/pub/pdb/validation_reports/y5/7y5j	HTTPS FTP

-
Related structure data

Related structure data	7y4xC 7y54C 7y5rC 7y6eC 7y6oC 7y73C 7y8hC 7y8iC 7y8sC 7y95C 7y9aC 6zr7S S: Starting model for refinement C: citing same article (ref.)

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Down Syndrome Cell Adhesion Molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	64.773, 64.773, 113.046
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-237- HOH
2	1	A-241- HOH

#1: Protein	Down Syndrome Cell Adhesion Molecules Mass: 11237.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.62 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 1 M Sodium citrate tribasic, 100 mM Sodium cacodylate/ Hydrochloric acid pH6.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9793 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 19264 / % possible obs: 100 % / Redundancy: 37.8 % / R_merge(I) obs: 0.092 / R_pim(I) all: 0.015 / R_rim(I) all: 0.094 / Χ²: 1.03 / Net I/σ(I): 6 / Num. measured all: 727817

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.6-1.63	35.9	1.016	940	0.936	0.171	1.031	0.965	100
1.63-1.66	39.1	0.855	939	0.957	0.138	0.867	0.977	100
1.66-1.69	39.3	0.731	933	0.965	0.118	0.741	1.032	100
1.69-1.72	39.1	0.568	926	0.982	0.092	0.576	1.046	100
1.72-1.76	38.4	0.53	944	0.982	0.086	0.537	1.043	100
1.76-1.8	37	0.406	946	0.99	0.067	0.412	1.102	100
1.8-1.85	37.5	0.327	940	0.991	0.054	0.332	1.122	100
1.85-1.9	38.9	0.262	940	0.999	0.043	0.266	1.184	100
1.9-1.95	39.6	0.213	952	0.996	0.035	0.216	1.196	100
1.95-2.02	39.1	0.18	948	0.997	0.029	0.182	1.207	100
2.02-2.09	38.6	0.16	949	0.998	0.026	0.162	1.18	100
2.09-2.17	36.5	0.142	949	0.997	0.024	0.144	1.122	100
2.17-2.27	37.6	0.13	947	0.997	0.021	0.132	1.074	100
2.27-2.39	39.5	0.116	973	0.998	0.019	0.118	0.986	100
2.39-2.54	38.8	0.109	959	0.998	0.018	0.111	0.96	100
2.54-2.74	37.7	0.098	974	0.999	0.016	0.099	0.897	100
2.74-3.01	36.8	0.092	978	0.998	0.015	0.093	0.916	100
3.01-3.45	38.7	0.087	990	0.996	0.014	0.088	0.932	100
3.45-4.34	35.3	0.081	1023	0.998	0.014	0.082	0.934	100
4.34-50	33.4	0.065	1114	0.999	0.011	0.066	0.737	99.8

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.15.2_3472	refinement
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ZR7

6zr7

Resolution: 1.6→21.202 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2141	920	4.79 %
R_work	0.1891	18272	-
obs	0.1903	19192	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 132.29 Å² / B_iso mean: 24.901 Å² / B_iso min: 5.03 Å²

Refinement step

Cycle: final / Resolution: 1.6→21.202 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	753	0	0	156	909
B_iso mean	-	-	-	33	-
Num. residues	-	-	-	-	95

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
1.6-1.6842	0.2761	121	0.2374	2537
1.6842-1.7897	0.233	121	0.219	2569
1.7897-1.9278	0.2194	137	0.208	2548
1.9278-2.1216	0.2358	122	0.1813	2586
2.1216-2.4282	0.2196	144	0.1866	2577
2.4282-3.0579	0.2147	145	0.2013	2633
3.0579-21.202	0.1863	130	0.1678	2822

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	3.3453	0.6508	-0.0679	2.7053	-0.8019	5.5301	-0.0696	0.1174	-0.2813	0.0545	0.0714	0.0185	0.18	-0.1937	-0.0097	0.1118	-0.0373	0.0227	0.0298	-0.0125	0.1181	18.7243	-22.3974	-5.2269
2	1.7444	-0.2868	0.0589	0.8285	-1.7072	3.6988	-0.0068	-0.0449	0.2686	-0.0824	0.0797	0.1186	-0.2241	-0.1146	-0.0053	0.2062	-0.0287	-0.019	0.0375	0.0161	0.0992	19.9949	-11.3347	-7.1715
3	7.0504	-3.2367	-7.4091	5.0072	2.5075	9.464	-0.1566	-0.2302	0.0767	0.0944	-0.0118	-0.3408	0.0817	0.7671	0.1841	0.064	-0.048	0.0213	0.1017	0.0208	0.128	28.6675	-14.8243	-9.1892
4	2.1108	-0.0177	-0.5298	1.6314	-0.7708	4.0173	0.0345	-0.2055	0.0015	0.1257	-0.0211	0.0242	-0.0005	-0.0851	0.0177	0.0946	-0.0316	0.0179	0.0416	0.0018	0.0643	18.9403	-17.3243	-0.5341
5	1.2894	1.7222	-1.5407	4.8172	-4.7655	5.4994	-0.1698	0.1543	0.133	-0.2359	0.0474	0.2574	0.0356	-0.1105	-0.2449	0.2214	-0.0604	-0.0323	0.0737	0.0874	0.1426	15.2294	-11.0098	-15.1478
6	1.9361	-0.3824	1.3117	2.7115	0.1289	4.7809	0.0481	-0.4957	-0.4324	0.2957	-0.015	0.143	0.3825	-0.1551	0.0384	0.1202	-0.0504	0.1154	0.1631	0.0727	0.1399	12.1835	-23.8475	4.7589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 2:26)	A	2 - 26
2	X-RAY DIFFRACTION	2	(chain A and resid 27:50)	A	27 - 50
3	X-RAY DIFFRACTION	3	(chain A and resid 51:57)	A	51 - 57
4	X-RAY DIFFRACTION	4	(chain A and resid 58:77)	A	58 - 77
5	X-RAY DIFFRACTION	5	(chain A and resid 78:90)	A	78 - 90
6	X-RAY DIFFRACTION	6	(chain A and resid 91:95)	A	91 - 95

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi