PDB-8vsh: Crystal structure of Shewanella benthica Group 1 truncated hemogl...

ID or keywords:

Entry

Database: PDB / ID: 8vsh

Title

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

Components

Group 1 truncated hemoglobin

Keywords

HEME-BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / HEME BINDING PROTEIN / PSYCHROPIEZOPHILE

Function / homology

Function and homology information

oxygen transport / oxygen binding / heme binding / metal ion binding
Similarity search - Function

Biological species

Shewanella benthica KT99 (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2 Å

Authors

Lecomte, J.T.J. / Martinez, J.E. / Schlessman, J.L. / Schultz, T.D. / Siegler, M.A.

Funding support

United States, 3items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	MCB-1330488	United States
National Science Foundation (NSF, United States)	CHE-2003950	United States
National Science Foundation (NSF, United States)	GRFP-1746891	United States

Citation

Journal: J.Inorg.Biochem. / Year: 2024
Title: Heme d formation in a Shewanella benthica hemoglobin.
Authors: Martinez Grundman, J.E. / Schultz, T.D. / Schlessman, J.L. / Liu, K. / Johnson, E.A. / Lecomte, J.T.J.

History

Deposition	Jan 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8vsh.cif.gz	197.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8vsh.ent.gz		Display	PDB format
PDBx/mmJSON format	8vsh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8vsh_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8vsh_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8vsh_validation.xml.gz	22.4 KB	Display
Data in CIF	8vsh_validation.cif.gz	29.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsh ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsh	HTTPS FTP

-
Related structure data

Related structure data	8ugzC 8w3aC 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
Related items in Molecule of the Month	#206 - Feb 2017 Globin Evolution similarity (2) #41 - May 2003 Hemoglobin similarity (5) #159 - Mar 2013 Erythrocruorin similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#206 - Feb 2017
Globin Evolution
similarity (2)
#41 - May 2003
Hemoglobin
similarity (5)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: Group 1 truncated hemoglobin

B: Group 1 truncated hemoglobin

C: Group 1 truncated hemoglobin

D: Group 1 truncated hemoglobin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	27.364, 104.604, 150.710
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Group 1 truncated hemoglobin Mass: 12838.427 Da / Num. of mol.: 4 / Mutation: C51S, C71S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Gene: KT99_16901 / Production host: Escherichia coli (E. coli) / References: UniProt: A9DF82
#2: Chemical	ChemComp-A1ADT / {3-[(2R,5'R)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosa[1,3(24),6,8,10,12,14,16(22),17,19]decaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato}iron Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 25% PEG MME 2000, 10 mM KCN, 18 days in the dark, 43 days exposed to laboratory ambient light

-
Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 17, 2023
Radiation	Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2→24.03 Å / Num. obs: 30478 / % possible obs: 99.9 % / Redundancy: 10.4 % / R_merge(I) obs: 0.034 / Net I/σ(I): 32.38
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.178 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3055 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5072	refinement
CrysalisPro	42.95a	data scaling
CrysalisPro	42.95a	data reduction
PHASER	1.21rc1_5072	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→24.03 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.76 / Phase error: 21.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.226	1994	6.56 %
R_work	0.1907	-	-
obs	0.193	30400	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→24.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3592	0	176	224	3992

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3884
X-RAY DIFFRACTION	f_angle_d	0.609	5320
X-RAY DIFFRACTION	f_dihedral_angle_d	11.779	1500
X-RAY DIFFRACTION	f_chiral_restr	0.039	564
X-RAY DIFFRACTION	f_plane_restr	0.003	680

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.05	0.2798	139	0.2061	1973	X-RAY DIFFRACTION	100
2.05-2.11	0.2826	143	0.2093	2034	X-RAY DIFFRACTION	100
2.11-2.17	0.25	136	0.1948	1939	X-RAY DIFFRACTION	100
2.17-2.24	0.215	141	0.1889	2004	X-RAY DIFFRACTION	100
2.24-2.32	0.2347	141	0.1919	2001	X-RAY DIFFRACTION	100
2.32-2.41	0.2485	140	0.1855	1986	X-RAY DIFFRACTION	100
2.41-2.52	0.2146	142	0.1851	2028	X-RAY DIFFRACTION	100
2.52-2.65	0.2391	140	0.1945	1992	X-RAY DIFFRACTION	100
2.65-2.82	0.2374	143	0.2049	2023	X-RAY DIFFRACTION	100
2.82-3.04	0.2223	142	0.2011	2050	X-RAY DIFFRACTION	100
3.04-3.34	0.2373	142	0.198	2011	X-RAY DIFFRACTION	100
3.34-3.82	0.1994	144	0.1782	2062	X-RAY DIFFRACTION	100
3.82-4.81	0.1981	145	0.1641	2076	X-RAY DIFFRACTION	100
4.81-24.03	0.2086	156	0.1981	2227	X-RAY DIFFRACTION	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	0.9747	0.8549	-0.5036	1.3727	0.1791	1.257	0.0821	-0.1576	0.0015	0.2502	-0.1244	-0.1063	0.0934	0.1498	-0.1478	0.0784	-0.0159	-0.0501	0.0645	0.0104	0.0909	10.9011	42.35	46.8625
2	0.6432	0.1469	-0.0096	0.2392	-0.0558	1.6521	0.0044	-0.1604	0.2179	0.1063	0.0516	-0.1083	-0.2097	0.1307	-0.055	0.0831	-0.0174	-0.0377	0.068	-0.0091	0.0929	11.3873	54.9813	33.0312
3	1.28	0.4411	-0.3901	0.9647	-0.3111	1.2063	0.041	-0.1676	0.1055	0.087	-0.0093	-0.0332	-0.0416	0.0242	0.073	0.0643	-0.0256	-0.0246	0.0815	-0.0241	0.0423	6.1604	49.531	47.7763
4	0.4406	-0.0022	0.212	0.8448	-0.1357	0.9017	0.0525	-0.0231	-0.0233	0.1352	-0.0026	-0.0408	0.0238	-0.0623	0.0549	0.0318	-0.0101	-0.0223	0.0408	-0.0133	0.047	3.1079	47.3166	38.1008
5	0.4351	-0.0386	0.3467	1.2474	0.0403	0.89	0.0909	-0.0354	-0.0505	0.1504	-0.0688	-0.0098	0.1859	-0.0143	-0.1002	0.0901	-0.0187	-0.0347	0.0383	-0.0195	0.0676	2.9456	37.7037	38.8802
6	0.6101	-0.2948	-0.0768	0.9026	-0.0005	1.174	0.0885	0.2036	0.1232	-0.2636	-0.0064	-0.0868	-0.241	0.0794	-0.0594	0.2227	-0.0021	0.1126	0.1818	0.0075	0.1133	10.9674	54.2955	-6.9687
7	0.4851	-0.0376	-0.0633	0.7206	-0.1472	1.0069	0.0056	0.2189	-0.1354	-0.1945	-0.0213	-0.0098	0.0469	-0.0325	0.0229	0.1232	0.0223	0.0593	0.1659	-0.0314	0.0816	8.8507	43.985	-1.4818
8	1.3643	2.7611	-1.238	6.5153	-1.5521	2.1032	-0.1179	0.5695	0.1564	-0.8969	0.0583	-0.0462	0.0013	-0.2175	-0.003	0.2365	0.0462	0.0279	0.3846	0.0367	0.168	-1.1423	48.7745	-11.167
9	0.6429	-0.3823	-0.2057	0.767	0.4364	1.2652	0.1501	0.1908	0.1258	-0.2307	-0.07	-0.0732	-0.3186	-0.1315	-0.0733	0.1312	0.0223	0.058	0.1173	0.007	0.094	3.8407	53.5049	3.4783
10	1.5252	-0.0596	0.6761	0.7664	0.3573	1.8669	0.1312	-0.0947	-0.2422	0.2295	-0.0944	0.032	0.3827	-0.1064	-0.4103	0.1732	-0.0913	-0.0174	0.1146	-0.016	0.0949	-5.6268	21.0572	25.9779
11	0.2409	0.0497	0.04	0.5499	0.103	0.3632	-0.0164	0.1626	-0.109	-0.0502	0.0075	-0.0205	0.0688	0.0145	-0.173	0.0833	-0.0347	-0.0246	0.1127	-0.0559	0.0931	-3.4248	26.6489	15.7467
12	1.2485	1.063	-2.6206	1.5017	-2.1729	5.998	-0.1424	0.0343	-0.518	-0.1394	0.0214	-0.2429	0.7736	0.0013	0.0918	0.181	0.0251	-0.0365	0.1006	-0.0209	0.2643	6.887	16.7746	20.5365
13	0.4145	0.0494	0.2773	0.8621	0.3028	0.9544	0.0488	-0.0161	-0.049	0.1549	-0.0213	-0.0202	0.1595	-0.0543	0.0016	0.0584	-0.0298	-0.0065	0.0706	-0.0258	0.0513	1.5354	31.6107	25.3352
14	0.8834	0.0414	-0.4366	1.0938	-0.0069	0.9704	0.1311	0.1892	0.3066	-0.2556	-0.0804	0.0333	-0.2452	-0.0882	-0.2235	0.1892	0.1118	0.0131	0.1148	0.0287	0.1558	-5.8984	74.9552	13.7996
15	0.4162	-0.3667	-0.0193	1.1215	0.2826	0.4478	0.0012	-0.034	0.1365	-0.0405	-0.0271	-0.0665	-0.0459	0.0125	-0.0619	0.0396	0.0302	0.0234	0.0495	0.0053	0.1198	-3.5635	69.1662	23.9732
16	1.0182	-0.8084	1.9797	1.3576	-1.4907	3.8569	-0.0602	0.1422	0.4282	-0.0253	-0.0099	-0.2355	-0.7437	-0.0021	0.1372	0.2393	0.0135	0.0622	0.0978	0.0328	0.3183	6.4175	79.2688	19.4398
17	0.5472	-0.1133	-0.2442	0.9168	0.2266	0.5624	0.1343	0.1518	0.1613	-0.3092	-0.1132	-0.0896	-0.1922	-0.0659	0.0801	0.1291	0.0643	0.0243	0.0917	0.0179	0.0758	1.4021	64.4335	14.4026

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 54 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 55 through 92 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 93 through 117 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 26 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 64 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 117 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 26 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 27 through 53 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 54 through 64 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 117 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 26 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 27 through 53 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 54 through 64 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 65 through 117 )

-
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