PDB-7k7u: BetaB2-crystallin

ID or keywords:

Entry

Database: PDB / ID: 7k7u

Title

BetaB2-crystallin

Components

Beta-crystallin B2

Keywords

STRUCTURAL PROTEIN / structural constituent of eye lens protein

Function / homology

Function and homology information

structural constituent of eye lens / lens development in camera-type eye / response to stimulus /

visual perception / structural molecule activity / identical protein binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.03 Å

Authors

Tan, L.L. / Jackson, C.J.

Citation

Journal: To Be Published
Title: BetaB2-crystallin
Authors: Jackson, C.J. / Carver, J.A. / Tan, L.L. / Grosas, A.B.

History

Deposition	Sep 24, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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	7k7u.cif.gz	878.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7k7u.ent.gz	740.7 KB	Display	PDB format
PDBx/mmJSON format	7k7u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k7/7k7u ftp://data.pdbj.org/pub/pdb/validation_reports/k7/7k7u	HTTPS FTP

-
Related structure data

Related structure data	1ytqS S: Starting model for refinement
Similar structure data	7k7u-3 7k7u-2 1ytq-3 6k0k-2 1blb-2 6fg5-d 1blb-1 2bb2-1 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

Related structure data

1ytqS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (5)

Deposited unit

I: Beta-crystallin B2

J: Beta-crystallin B2

K: Beta-crystallin B2

L: Beta-crystallin B2

A: Beta-crystallin B2

C: Beta-crystallin B2

D: Beta-crystallin B2

E: Beta-crystallin B2

B: Beta-crystallin B2

F: Beta-crystallin B2

G: Beta-crystallin B2

H: Beta-crystallin B2

281 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

I: Beta-crystallin B2

J: Beta-crystallin B2

K: Beta-crystallin B2

L: Beta-crystallin B2

defined by author&software
Evidence: light scattering, The tetrameric assembly (oligomeric state) was confirmed using size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS)
93.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Beta-crystallin B2

C: Beta-crystallin B2

D: Beta-crystallin B2

E: Beta-crystallin B2

defined by author&software
93.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Beta-crystallin B2

F: Beta-crystallin B2

G: Beta-crystallin B2

H: Beta-crystallin B2

defined by author&software
93.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.655, 113.192, 340.234
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Beta-crystallin B2 / Beta-B2 crystallin / Beta-crystallin Bp Mass: 23411.932 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBB2, CRYB2, CRYB2A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43320
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.7 Å³/Da / Density % sol: 58.53 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 10% w/v PEG 8,000, 8% (v/v) ethylene glycol PH range: 7.0 - 8.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.03→47.16 Å / Num. obs: 59687 / % possible obs: 99.3 % / Redundancy: 6.3 % / B_iso Wilson estimate: 68.16 Å² / CC_1/2: 0.992 / Χ²: 0.99 / Net I/σ(I): 8.5
Reflection shell	Resolution: 3.03→3.11 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.8 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4370 / CC_1/2: 0.316 / R_pim(I) all: 0.771 / Χ²: 0.96 / % possible all: 95.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YTQ

1ytq

Resolution: 3.03→45 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.891 / SU B: 54.563 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25037	2971	5 %	RANDOM
R_work	0.18894	-	-	-
obs	0.19202	56644	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 72.608 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.02 Å²	-0 Å²	0 Å²
2-	-	1 Å²	0 Å²
3-	-	-	2.02 Å²

Refinement step

Cycle: 1 / Resolution: 3.03→45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18024	0	0	62	18086

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	18544
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	16660
X-RAY DIFFRACTION	r_angle_refined_deg	1.719	1.646	25094
X-RAY DIFFRACTION	r_angle_other_deg	1.188	1.585	38554
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.649	5	2209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.765	22.96	1098
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.42	15	3097
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.835	15	110
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	2197
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	21377
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4515
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.602	5.194	8872
X-RAY DIFFRACTION	r_mcbond_other	3.602	5.194	8871
X-RAY DIFFRACTION	r_mcangle_it	6.283	7.772	11069
X-RAY DIFFRACTION	r_mcangle_other	6.282	7.772	11070
X-RAY DIFFRACTION	r_scbond_it	3.047	5.555	9672
X-RAY DIFFRACTION	r_scbond_other	3.047	5.555	9673
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.46	8.175	14026
X-RAY DIFFRACTION	r_long_range_B_refined	12.687	96.661	71821
X-RAY DIFFRACTION	r_long_range_B_other	12.686	96.666	71815
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.032→3.111 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.385	206	-
R_work	0.359	3945	-
obs	-	-	95.62 %

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	2.7603	0.0556	0.3944	0.4025	0.1319	0.3556	-0.0332	-0.3534	0.0052	0.2082	-0.0076	-0.0629	-0.1208	-0.1727	0.0407	0.4228	0.098	0.0119	0.217	-0.0329	0.1153	-21.02	-28.331	39.597
2	2.0981	-0.1768	0.6055	0.2858	-0.1473	0.9712	-0.1327	0.3976	-0.0106	-0.0807	0.0659	-0.0808	-0.0227	-0.1786	0.0668	0.3649	-0.0671	-0.0093	0.2629	-0.0307	0.0999	-20.495	-27.815	10.338
3	3.4019	0.2144	0.2064	0.7577	-0.1458	0.4903	-0.0758	0.1659	0.4694	-0.0193	0.0051	-0.0821	-0.2799	-0.0514	0.0706	0.3744	0.0334	-0.0617	0.023	-0.0131	0.2909	-9.156	-13.705	22.637
4	1.9802	-0.4454	0.1411	0.346	-0.2139	0.7421	-0.1467	-0.1348	-0.2605	0.044	0.0822	-0.072	0.1619	-0.1207	0.0645	0.3721	0.0008	0.0506	0.0297	-0.0182	0.3761	-9.997	-42.655	27.631
5	3.1187	0.1916	0.2891	0.3437	0.0173	0.9354	0.0843	0.488	-0.0335	-0.0525	0.0621	0.0672	0.0455	0.2521	-0.1464	0.2747	0.0278	0.0148	0.2721	-0.0764	0.1347	31.053	27.96	17.462
6	2.9202	0.2521	0.6947	0.5743	0.0419	0.5648	0.0684	-0.0396	0.4125	0.0741	-0.0654	0.1673	-0.0849	0.0877	-0.0029	0.2738	-0.0146	0.0376	0.038	-0.0421	0.3372	16.612	43.257	31.329
7	3.1224	0.8624	0.6226	0.6706	0.2364	1.0333	0.1247	0.0605	-0.4115	0.0631	-0.0112	0.0184	0.3361	0.1021	-0.1134	0.344	0.0347	-0.0423	0.0158	-0.0498	0.3568	19.507	14.207	30.115
8	3.2112	0.3002	0.4407	0.2003	-0.02	1.1694	0.1247	-0.5297	0.1099	0.2234	-0.0286	0.0888	0.0379	0.0805	-0.0961	0.357	0.0081	-0.0015	0.2533	-0.0674	0.1793	27.824	31.658	46.265
9	3.448	-0.2949	0.1516	0.3366	0.1528	0.8653	0.0219	-0.6137	0.0307	0.0648	0.0243	0.0082	0.1004	0.0557	-0.0462	0.3126	0.0182	-0.0101	0.2971	0.0063	0.0822	25.599	-18.654	96.845
10	3.6186	0.0245	0.2312	0.2697	0.0468	0.8956	0.1252	0.0407	-0.6113	0.0007	0.0146	0.0347	0.327	-0.0271	-0.1398	0.3659	-0.0008	-0.0463	0.0085	-0.0199	0.3434	11.283	-33.473	82.283
11	3.4563	-0.4819	-0.0608	1.0031	0.3054	0.5381	0.0362	-0.2201	0.3021	-0.0925	-0.1116	0.0717	-0.2042	0.0523	0.0754	0.3994	0.0375	-0.0218	0.0916	-0.076	0.2223	14.828	-4.292	84.053
12	2.208	-0.1264	0.0656	0.1401	0.0074	1.2449	0.0621	0.2383	-0.2431	-0.1542	0.0093	0.0932	0.093	0.2079	-0.0714	0.4397	0.0181	-0.0095	0.1638	-0.093	0.1696	22.98	-21.952	67.884
13	0.008	0.0167	-0.0187	0.0514	-0.0348	0.0597	0.0199	0.0111	0.0199	0.056	0.012	0.1314	-0.0018	0.0144	-0.0319	0.3436	0.048	0.0042	0.1902	0.0024	0.6014	7.874	-1.594	48.58

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	I	13 - 196
2	X-RAY DIFFRACTION	2	J	13 - 194
3	X-RAY DIFFRACTION	3	K	11 - 196
4	X-RAY DIFFRACTION	4	L	13 - 194
5	X-RAY DIFFRACTION	5	A	12 - 194
6	X-RAY DIFFRACTION	6	C	12 - 194
7	X-RAY DIFFRACTION	7	D	12 - 194
8	X-RAY DIFFRACTION	8	E	13 - 194
9	X-RAY DIFFRACTION	9	B	11 - 194
10	X-RAY DIFFRACTION	10	F	11 - 194
11	X-RAY DIFFRACTION	11	G	12 - 195
12	X-RAY DIFFRACTION	12	H	13 - 195
13	X-RAY DIFFRACTION	13	A	301 - 309
14	X-RAY DIFFRACTION	13	B	301 - 304
15	X-RAY DIFFRACTION	13	C	301 - 309
16	X-RAY DIFFRACTION	13	D	301 - 303
17	X-RAY DIFFRACTION	13	E	301 - 305
18	X-RAY DIFFRACTION	13	F	301 - 305
19	X-RAY DIFFRACTION	13	G	301 - 304
20	X-RAY DIFFRACTION	13	H	301 - 309
21	X-RAY DIFFRACTION	13	I	301 - 305
22	X-RAY DIFFRACTION	13	J	301 - 302
23	X-RAY DIFFRACTION	13	K	301 - 303
24	X-RAY DIFFRACTION	13	L	301 - 304

-
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://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