PDB-8fnr: X-ray crystal structure of Hansschlegelia quercus lanmodulin (Lan...

ID or keywords:

Entry

Database: PDB / ID: 8fnr

Title

X-ray crystal structure of Hansschlegelia quercus lanmodulin (LanM) with dysprosium (III) bound at pH 7

Components

EF-hand domain-containing protein

Keywords

METAL BINDING PROTEIN / methanol dehydrogenase

Function / homology

EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / calcium ion binding / : / EF-hand domain-containing protein

Function and homology information

Biological species

Hansschlegelia quercus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Jung, J.J. / Lin, C.-Y. / Boal, A.K.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2023
Title: Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.
Authors: Mattocks, J.A. / Jung, J.J. / Lin, C.Y. / Dong, Z. / Yennawar, N.H. / Featherston, E.R. / Kang-Yun, C.S. / Hamilton, T.A. / Park, D.M. / Boal, A.K. / Cotruvo Jr., J.A.

History

Deposition	Dec 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 26, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8fnr.cif.gz	200.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8fnr.ent.gz	158.2 KB	Display	PDB format
PDBx/mmJSON format	8fnr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8fnr_validation.pdf.gz	10 MB	Display	wwPDB validaton report
Full document	8fnr_full_validation.pdf.gz	10.1 MB	Display
Data in XML	8fnr_validation.xml.gz	24.5 KB	Display
Data in CIF	8fnr_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fn/8fnr ftp://data.pdbj.org/pub/pdb/validation_reports/fn/8fnr	HTTPS FTP

-
Related structure data

Related structure data	8dq2C 8fnsC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: EF-hand domain-containing protein

B: EF-hand domain-containing protein

C: EF-hand domain-containing protein

D: EF-hand domain-containing protein

hetero molecules

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

1

A: EF-hand domain-containing protein

B: EF-hand domain-containing protein

hetero molecules

defined by author&software
25 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: EF-hand domain-containing protein

D: EF-hand domain-containing protein

hetero molecules

defined by author&software
25 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.000, 54.234, 65.275
Angle α, β, γ (deg.)	90.000, 93.570, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	EF-hand domain-containing protein Mass: 11923.299 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hansschlegelia quercus (bacteria) / Gene: EYR15_14300 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4V2JDD3
#2: Chemical	ChemComp-DY / DYSPROSIUM ION Mass: 162.500 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Dy / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.7 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 250 uM tri-sodium citrate, pH 7, and 27 % (w/v) PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9792 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.4→50 Å / Num. obs: 138347 / % possible obs: 91.61 % / Redundancy: 7.5 % / CC_1/2: 0.997 / Net I/σ(I): 27.972
Reflection shell	Resolution: 1.4→1.45 Å / Num. unique obs: 8026 / CC_1/2: 0.74

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.4→27.41 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1808	3636	2.63 %
R_work	0.1613	134760	-
obs	0.1619	138326	91.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 83.62 Å² / B_iso mean: 25.9592 Å² / B_iso min: 8.77 Å²

Refinement step

Cycle: final / Resolution: 1.4→27.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3295	0	14	623	3932
B_iso mean	-	-	20.03	35.47	-
Num. residues	-	-	-	-	435

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4-1.42	0.2554	57	0.2311	2117	2174	37
1.42-1.44	0.2161	91	0.2156	3172	3263	56
1.44-1.46	0.2285	104	0.2116	3557	3661	64
1.46-1.48	0.2092	94	0.2095	4127	4221	72
1.48-1.5	0.2303	125	0.205	4496	4621	78
1.5-1.52	0.2147	143	0.2004	4796	4939	84
1.52-1.55	0.2181	137	0.1936	5053	5190	89
1.55-1.58	0.2025	133	0.1802	5442	5575	96
1.58-1.61	0.1797	156	0.1814	5577	5733	99
1.61-1.64	0.1773	158	0.1798	5696	5854	100
1.64-1.68	0.1966	152	0.1751	5642	5794	100
1.68-1.72	0.1933	141	0.1689	5694	5835	100
1.72-1.76	0.2026	155	0.1659	5740	5895	100
1.76-1.81	0.1637	157	0.1668	5731	5888	100
1.81-1.86	0.2077	174	0.163	5613	5787	100
1.86-1.92	0.1532	124	0.1598	5717	5841	100
1.92-1.99	0.1628	183	0.1535	5657	5840	100
1.99-2.07	0.1806	144	0.1504	5720	5864	100
2.07-2.16	0.1471	168	0.1515	5658	5826	100
2.16-2.28	0.1946	149	0.1508	5654	5803	100
2.28-2.42	0.2184	139	0.1607	5726	5865	100
2.42-2.61	0.1672	151	0.1586	5717	5868	100
2.61-2.87	0.1868	156	0.169	5665	5821	100
2.87-3.28	0.1754	138	0.1675	5690	5828	100
3.28-4.13	0.1684	155	0.1414	5680	5835	100
4.14-27.41	0.169	152	0.1473	5423	5575	95

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	5.5697	0.8862	0.8536	1.0868	0.0787	1.5939	0.0623	-0.2944	-0.3512	0.0464	-0.0293	-0.0935	0.2696	0.0834	-0.0038	0.2128	0.043	0.0043	0.1215	0.0231	0.1085	26.5982	-20.1095	30.7135
2	5.9502	1.6207	2.1858	1.6701	2.1467	2.7696	-0.1388	0.5928	-0.0808	-0.3485	0.073	-0.1135	-0.0044	0.3506	0.0816	0.2513	0.012	0.0438	0.206	0.0392	0.1287	32.9593	-17.2226	23.2918
3	4.0853	-1.4535	-4.523	9.0484	-1.7164	7.4819	-0.2386	0.7002	0.442	0.0007	0.0009	0.3044	-1.0138	0.2157	0.2154	0.299	-0.011	-0.115	0.6748	0.0621	0.3447	-7.4064	-12.3832	24.9163
4	7.5458	-3.1835	4.5953	2.7343	-2.3671	4.7049	0.0385	1.3907	-0.3964	-1.1223	-0.0605	0.9784	-0.0564	-0.424	0.1279	0.485	-0.2114	-0.1539	0.6967	0.0584	0.4157	-3.2912	-17.0258	19.416
5	4.7933	1.0927	0.2717	3.6386	0.9155	3.5529	-0.1048	-0.2645	0.171	0.2162	0.1455	0.1281	-0.0364	-0.0641	-0.0409	0.1426	0.0278	-0.0047	0.1254	0.0215	0.1603	9.1823	-11.8575	34.1853
6	3.8074	0.005	-0.5513	3.5111	0.6182	2.9625	-0.1211	-0.238	-0.5915	0.0815	0.0233	0.2248	0.4781	-0.3444	-0.0462	0.2297	-0.0274	0.0325	0.1463	0.0296	0.1988	5.5605	-21.0048	31.6396
7	4.3326	-2.1317	0.319	3.8759	4.0231	6.2102	-0.4757	-0.0215	0.3735	-0.2747	0.0296	0.6713	0.0867	-0.7989	0.0812	0.1623	-0.0249	-0.044	0.2517	0.0369	0.2526	-1.2288	-14.5598	31.8372
8	8.4233	3.4579	0.7929	5.4571	-0.0098	4.3873	0.0289	-0.9796	-0.2646	0.668	0.0132	0.5856	0.2709	-0.6163	0.0362	0.1944	0.0108	0.0657	0.2709	0.0882	0.3321	-3.6089	-0.8176	13.1151
9	3.1669	-0.0398	-0.196	2.1588	0.7221	2.1117	-0.0368	0.3621	-0.2257	-0.2616	0.1374	-0.1047	-0.0519	0.1284	-0.078	0.0912	-0.0283	-0.0085	0.0918	-0.016	0.1283	11.8296	-4.829	-2.6934
10	2.8167	-1.826	-0.2859	2.4977	0.8587	1.8336	0.015	0.1143	0.0398	-0.0959	-0.0143	0.1247	-0.1115	-0.0821	0	0.0881	-0.0054	-0.0205	0.0617	0.0311	0.1123	2.419	3.5504	2.6818
11	6.8989	1.0703	1.0478	5.1784	-4.3191	4.167	-0.4404	-0.962	-0.6277	1.6292	-0.256	0.0441	0.2409	0.362	0.4139	0.6569	0.1752	0.1228	0.3564	0.0955	0.3129	36.8816	-10.3061	10.0552
12	7.6122	-4.5007	-0.8623	6.4381	2.2822	4.1966	0.184	0.264	-1.3284	0.1257	-0.2519	0.3066	1.2779	0.622	0.0356	0.3288	0.0788	0.0226	0.3451	-0.0379	0.3769	35.054	-12.3059	2.0394
13	3.0723	-0.3051	-0.1061	1.0896	-0.0469	2.1919	0.08	-0.3065	0.1139	0.0921	-0.0561	-0.0964	-0.1934	0.1385	0.0071	0.1168	-0.0403	-0.0088	0.1243	-0.0014	0.1198	21.1833	2.0458	13.8865
14	4.6196	-1.0496	-0.8873	1.4095	0.4664	2.3324	0.0965	0.0518	0.2363	-0.1129	-0.0313	-0.1529	-0.1942	0.2848	-0.0552	0.117	-0.0471	0.0018	0.114	0.0179	0.1015	27.2331	2.5111	6.4977
15	4.1406	-0.7052	-1.3838	6.9034	-4.6096	3.9243	-0.0994	1.0064	0.4312	-1.8809	-0.345	-0.4526	-0.5293	0.1187	0.4321	0.5464	-0.045	-0.0014	0.3091	0.0679	0.2926	35.4605	-8.4455	22.0115
16	6.6082	1.9233	0.4519	7.1299	-0.7543	4.6485	-0.0358	-0.2585	1.0051	0.2588	-0.2584	0.1917	-1.5121	0.315	0.3133	0.4622	-0.0664	-0.091	0.2394	-0.0137	0.3174	33.7833	-5.5728	30.1051
17	4.4333	0.2778	1.6358	0.4973	-0.3476	3.3227	-0.0701	0.614	0.1343	-0.1984	-0.0072	0.0559	0.0521	0.2027	0.0789	0.2199	0.0198	0.004	0.1609	0.029	0.1384	19.7896	-17.7522	18.337
18	4.8635	-0.4504	-0.0236	2.9053	-0.0185	3.7283	0.1483	0.2416	-1.1889	-0.0053	0.0047	-0.243	0.9916	0.1923	-0.0461	0.445	-0.0105	-0.0383	0.1936	-0.052	0.356	16.241	-29.6582	21.1478

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 92 through 115 )	C	92 - 115
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 116 through 133 )	C	116 - 133
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 24 through 30 )	D	24 - 30
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 31 through 42 )	D	31 - 42
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 43 through 82 )	D	43 - 82
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 83 through 121 )	D	83 - 121
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 122 through 133 )	D	122 - 133
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 24 through 42 )	A	24 - 42
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 43 through 91 )	A	43 - 91
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 92 through 133 )	A	92 - 133
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 32 )	B	24 - 32
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 42 )	B	33 - 42
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 43 through 82 )	B	43 - 82
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 133 )	B	83 - 133
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 24 through 32 )	C	24 - 32
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 33 through 42 )	C	33 - 42
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 43 through 75 )	C	43 - 75
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 76 through 91 )	C	76 - 91

-
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