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

ID or keywords:

Entry

Database: PDB / ID: 8uzu

Title

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin L80A C51S C71S variant

Components

Group 1 truncated hemoglobin

Keywords

HEME-BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / 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: 1.9 Å

Authors

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

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.Biol.Chem. / Year: 2025
Title: Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N.
Authors: Martinez Grundman, J.E. / Schultz, T.D. / Schlessman, J.L. / Johnson, E.A. / Gillilan, R.E. / Lecomte, J.T.J.

History

Deposition	Nov 16, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details 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 / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uz/8uzu ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uzu	HTTPS FTP

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Related structure data

Related structure data	7tt9C 8tlsC 8vijC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#206 - Feb 2017 Globin Evolution similarity (3) #41 - May 2003 Hemoglobin similarity (5) #111 - Mar 2009 Hydrogenase similarity (1) #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 (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#206 - Feb 2017
Globin Evolution
similarity (3)
#41 - May 2003
Hemoglobin
similarity (5)
#111 - Mar 2009
Hydrogenase
similarity (1)
#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 (2)

Deposited unit

A: Group 1 truncated hemoglobin

B: Group 1 truncated hemoglobin

C: Group 1 truncated hemoglobin

D: Group 1 truncated hemoglobin

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	27.157, 105.221, 151.130
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: 12796.347 Da / Num. of mol.: 4 / Mutation: C51S, C71S, L80A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Strain: KT99 / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-CYN / CYANIDE ION Mass: 26.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CN
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 23% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN PH range: 5.1-6.0 / Temp details: Room Temp

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å
Detector	Type: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 23, 2022 / Details: NULL
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→22.99 Å / Num. obs: 35447 / % possible obs: 99.9 % / Redundancy: 5.6 % / R_merge(I) obs: 0.041 / R_sym value: 0.063 / Net I/σ(I): 24.41
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.16 / Mean I/σ(I) obs: 5.53 / Num. unique obs: 3551 / R_sym value: 0.203 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5072)	refinement
CrysalisPro	1.171.42.49	data scaling
PHASER	(1.21rc1_5072)	phasing
CrysalisPro	1.171.42.49	data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.9→22.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 21.89 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2238	1968	5.65 %
R_work	0.1951	-	-
obs	0.1967	34829	98.42 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→22.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3580	0	180	365	4125

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4010
X-RAY DIFFRACTION	f_angle_d	0.631	5496
X-RAY DIFFRACTION	f_dihedral_angle_d	12.506	1572
X-RAY DIFFRACTION	f_chiral_restr	0.043	574
X-RAY DIFFRACTION	f_plane_restr	0.005	713

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 (%)
1.9-1.95	0.2648	139	0.2241	2304	X-RAY DIFFRACTION	98
1.95-2	0.2586	134	0.2167	2201	X-RAY DIFFRACTION	96
2-2.06	0.2603	139	0.2087	2291	X-RAY DIFFRACTION	98
2.06-2.13	0.2284	135	0.1971	2303	X-RAY DIFFRACTION	98
2.13-2.2	0.2162	137	0.1965	2272	X-RAY DIFFRACTION	97
2.2-2.29	0.2311	141	0.1914	2352	X-RAY DIFFRACTION	99
2.29-2.39	0.2459	138	0.2023	2281	X-RAY DIFFRACTION	98
2.39-2.52	0.252	142	0.1997	2365	X-RAY DIFFRACTION	99
2.52-2.68	0.2865	140	0.2083	2325	X-RAY DIFFRACTION	99
2.68-2.88	0.2312	135	0.2126	2352	X-RAY DIFFRACTION	99
2.88-3.17	0.198	145	0.19	2389	X-RAY DIFFRACTION	99
3.17-3.63	0.2248	142	0.1865	2396	X-RAY DIFFRACTION	99
3.63-4.57	0.1606	150	0.1612	2471	X-RAY DIFFRACTION	99
4.57-22.99	0.2061	151	0.1976	2559	X-RAY DIFFRACTION	99

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	0.2833	-0.1813	-0.0267	0.5186	-0.0186	0.1262	0.0065	-0.0193	-0.0066	-0.0226	0.0158	0.0086	0.0315	0.0162	0.064	0.0377	0.0238	-0.0242	0.0317	-0.014	0.0739	16.8352	35.3414	99.371
2	0.527	-0.1012	-0.9117	0.1334	0.0121	1.8103	-0.0549	0.1406	-0.258	0.1003	-0.0523	0.1844	0.5612	-0.0142	0.1775	0.1828	0.0157	-0.0097	0.0993	-0.0718	0.2926	7.1775	25.485	96.3624
3	0.2538	-0.3714	0.0608	0.8139	0.1603	0.2422	0.0624	0.0881	-0.136	-0.2634	-0.1413	0.1351	-0.0244	-0.0052	-0.0026	0.1108	0.0229	0.0112	0.0498	-0.0112	0.0734	13.1737	42.2935	94.4907
4	0.0567	-0.1642	-0.1747	0.4735	0.5036	0.5349	0.1045	0.119	-0.0099	-0.5118	-0.1239	0.0948	-0.0909	-0.037	0.0917	0.388	0.0661	-0.0694	0.1185	-0.0285	0.1517	11.1634	38.1413	85.2838
5	0.2921	0.3648	0.1525	0.5803	0.4111	0.4659	0.0299	0.0382	0.0184	0.0639	-0.0704	0.0799	0.0064	-0.1148	-0.0562	0.0623	-0.0052	0.0429	0.0493	-0.016	0.0513	2.7249	62.6408	122.7783
6	1.59	0.0696	-0.2454	0.798	0.8755	2.7564	-0.0094	0.077	-0.1431	0.0995	-0.0281	0.0957	0.1789	-0.2284	-0.0928	0.0546	-0.026	0.0268	0.0717	-0.0151	0.0805	2.3911	49.8017	108.8894
7	2.367	0.4997	1.1593	1.5275	0.6166	2.6883	0.1738	-0.0926	-0.1273	0.0775	0.0079	-0.0281	0.2176	-0.041	0.0548	0.0825	-0.0084	0.001	0.0849	-0.0065	0.022	7.2509	54.5813	123.5126
8	0.3908	-0.1722	-0.2115	0.6938	0.524	1.0153	0.054	-0.0289	0.0636	0.0546	0.0441	-0.0609	-0.1316	0.1391	-0.0765	0.0844	0.0066	0.0144	0.0565	-0.0117	0.0386	10.2073	57.6342	113.9679
9	0.0546	-0.1374	-0.0543	0.6166	0.1829	0.0613	0.0413	-0.0139	0.0028	-0.0767	-0.0022	0.0242	-0.1341	0.0296	-0.0242	0.2156	-0.0543	0.0219	0.0584	-0.0056	0.0919	10.8772	67.1567	114.2069
10	0.2306	-0.0136	0.0408	0.1852	-0.0039	0.2211	0.0708	-0.0676	-0.0764	-0.0215	0.016	0.0174	0.1396	-0.0359	0.3001	0.0803	-0.0169	-0.0491	0.0868	-0.0058	0.0503	2.7434	50.6904	68.671
11	0.9366	-0.2024	0.1629	0.951	0.3593	1.0938	0.0321	0.0893	0.1707	-0.135	0.0225	-0.0534	-0.0743	-0.0768	0.0139	0.0726	0.0153	-0.0273	0.098	0.0127	0.0678	5.2378	60.373	73.7752
12	0.2456	-0.1231	-0.0696	2.8452	0.4793	0.6412	0.055	0.3012	-0.0959	-0.5734	-0.1019	0.0593	-0.0455	-0.0083	0.0878	0.2352	-0.0401	0.0105	0.2893	-0.046	0.0876	15.0203	56.9515	64.2215
13	0.192	0.1922	0.3155	0.3654	0.5568	1.4118	0.0996	0.0569	-0.09	-0.0094	0.0486	-0.0446	0.509	0.091	-0.1241	0.1881	-0.0014	-0.0526	0.0822	-0.0085	0.1036	9.9616	51.5385	79.1756
14	1.7687	-0.4974	-1.5828	1.0026	-0.028	2.3198	0.1795	-0.1465	0.2602	0.2302	-0.0207	-0.1815	-0.4153	0.1189	-0.1622	0.1439	-0.0483	-0.0082	0.0967	0.0007	0.1057	19.2576	83.5923	101.4758
15	0.9393	0.1074	0.065	1.2059	0.3028	1.371	0.0417	0.0702	0.1314	-0.0349	-0.0189	-0.0427	-0.156	-0.0934	0.0304	0.0344	-0.0141	0.0116	0.0648	-0.0007	0.0685	16.7355	78.6643	91.7521
16	0.6533	0.8729	1.5132	1.2084	1.9778	3.5521	-0.0832	-0.0964	0.323	-0.2364	-0.0224	0.1736	-0.6256	-0.0332	-0.0241	0.2763	-0.0112	-0.0814	0.1005	-0.0184	0.2607	6.5785	88.1701	94.9621
17	0.1421	0.1169	-0.1158	1.0355	0.4104	0.3668	0.0559	-0.0968	0.056	0.4031	-0.1311	0.0879	-0.0244	0.0137	0.0057	0.1673	-0.0363	0.0057	0.0919	0.0046	0.0718	11.7198	73.202	100.5765
18	0.8643	0.3674	0.616	2.0206	0.451	1.0987	0.115	0.1431	-0.1128	-0.415	-0.0204	-0.0688	0.1295	0.0577	-0.0955	0.1636	0.0512	-0.0086	0.0725	-0.0169	0.124	19.5532	30.1646	89.811

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 27 through 54 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 55 through 64 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 65 through 92 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 93 through 117 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 2 through 26 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 27 through 38 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 39 through 54 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 55 through 92 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 93 through 117 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 26 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 27 through 54 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 55 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 117 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 26 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 27 through 54 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 55 through 64 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 65 through 117 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 2 through 26 )

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