PDB-8w3a: Crystal structure of Shewanella benthica Group 1 truncated hemogl...

ID or keywords:

Entry

Database: PDB / ID: 8w3a

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 /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

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

Funding support

United States, 1items

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	Feb 22, 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

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PDBx/mmCIF format	8w3a.cif.gz	207.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8w3a_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	8w3a_full_validation.pdf.gz	3 MB	Display
Data in XML	8w3a_validation.xml.gz	23.9 KB	Display
Data in CIF	8w3a_validation.cif.gz	31 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/8w3a ftp://data.pdbj.org/pub/pdb/validation_reports/w3/8w3a	HTTPS FTP

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Related structure data

Related structure data	8ugzC 8vshC 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 (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 /

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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

56.3 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)	27.357, 104.809, 150.551
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 40.5 %
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

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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 25, 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: 1.8→24.25 Å / Num. obs: 41341 / % possible obs: 99.5 % / Redundancy: 6.8 % / R_merge(I) obs: 0.032 / Net I/σ(I): 54.01
Reflection shell	Resolution: 1.8→1.87 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.278 / Mean I/σ(I) obs: 3.97 / Num. unique obs: 4135 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207: 000	refinement
CrysalisPro	42.95a	data scaling
CrysalisPro	42.95a	data reduction
PHASER	1.21_5207: 000	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→24.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 22.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2359	1982	4.84 %
R_work	0.1981	-	-
obs	0.1999	40960	98.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→24.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3592	0	348	202	4142

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4190
X-RAY DIFFRACTION	f_angle_d	0.659	5810
X-RAY DIFFRACTION	f_dihedral_angle_d	12.022	1644
X-RAY DIFFRACTION	f_chiral_restr	0.041	582
X-RAY DIFFRACTION	f_plane_restr	0.004	723

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 (%)
1.8-1.84	0.3298	138	0.2567	2683	X-RAY DIFFRACTION	97
1.85-1.89	0.2763	135	0.2468	2654	X-RAY DIFFRACTION	98
1.89-1.95	0.2867	143	0.2285	2779	X-RAY DIFFRACTION	99
1.95-2.01	0.2689	138	0.2187	2696	X-RAY DIFFRACTION	99
2.01-2.09	0.2422	141	0.2261	2778	X-RAY DIFFRACTION	99
2.09-2.17	0.2496	138	0.2049	2736	X-RAY DIFFRACTION	100
2.17-2.27	0.234	143	0.1958	2804	X-RAY DIFFRACTION	99
2.27-2.39	0.2531	138	0.1999	2739	X-RAY DIFFRACTION	99
2.39-2.54	0.2477	143	0.201	2796	X-RAY DIFFRACTION	99
2.54-2.73	0.2578	143	0.2044	2828	X-RAY DIFFRACTION	99
2.73-3.01	0.2589	142	0.2058	2797	X-RAY DIFFRACTION	99
3.01-3.44	0.2245	143	0.1962	2824	X-RAY DIFFRACTION	99
3.44-4.33	0.189	145	0.1641	2851	X-RAY DIFFRACTION	99
4.33-24.25	0.1953	152	0.1755	3013	X-RAY DIFFRACTION	98

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	0.5985	0.0016	-0.0847	1.6608	-0.1702	0.5668	0.1496	-0.0983	0.0611	0.3121	-0.0627	0.1216	-0.1908	0.0855	-0.0066	0.145	-0.053	0.0216	0.1131	0.0012	0.0942	12.3521	12.2054	60.5321
2	1.3678	-0.984	-0.8743	1.9128	0.0351	1.0715	0.0466	0.1196	0.1285	-0.2364	-0.0566	-0.0292	-0.0022	-0.2758	-0.0931	0.1275	0.0272	-0.0768	0.0804	-0.0079	0.1253	2.7053	-10.0561	28.3789
3	1.0194	0.0844	-1.0397	1.4141	-0.4683	1.4673	-0.0989	0.0051	0.0972	-0.1582	-0.0172	-0.1151	-0.4754	-0.3987	0.1141	0.1842	0.0329	-0.0539	0.1201	-0.0121	0.1111	2.3157	2.6788	42.264
4	5.2372	-1.7586	-2.2535	2.3898	1.9196	3.4339	0.0601	0.0951	0.3435	0.1052	0.0661	-0.1095	-0.1181	0.007	-0.0683	0.1063	-0.0156	-0.0207	0.1029	0.0298	0.0709	7.2952	-2.1119	27.5713
5	0.8821	0.4321	0.3482	1.5556	0.4992	2.2891	0.096	-0.0141	-0.0109	-0.0686	-0.014	0.0244	-0.0265	0.1087	-0.048	0.0507	0.02	-0.0201	0.0467	0.0146	0.0879	10.4154	-5.1108	37.1948
6	0.6558	-0.2998	0.1321	2.0084	-0.1942	1.3795	0.0436	-0.0131	-0.1695	-0.2367	0.0235	-0.2205	0.2525	0.0509	-0.0469	0.1485	0.0175	-0.0261	0.0665	0.0348	0.0913	10.7078	-14.6007	36.4486
7	0.9828	0.1953	0.2806	0.9729	0.6487	0.4672	0.1076	-0.1379	0.0258	0.1501	-0.0381	0.0703	-0.3675	-0.1587	0.1503	0.2531	-0.0173	0.0804	0.1618	-0.0061	0.095	2.8018	2.0407	82.2173
8	1.8597	0.6329	-0.3929	1.6136	0.4642	2.3972	0.0683	-0.1267	-0.2731	0.3474	-0.0394	-0.0942	0.2423	0.0009	0.0315	0.1768	-0.0284	0.0305	0.1436	0.029	0.127	5.1773	-7.8763	77.0205
9	1.022	-0.4681	-0.1148	0.7279	-0.1962	0.1331	-0.2837	-0.6358	0.3903	0.93	-0.0085	0.1698	0.179	-0.1533	-0.3836	0.4985	0.0376	-0.0466	0.3844	-0.1113	0.1557	15.1718	-4.3182	86.528
10	0.6375	0.2202	-0.4147	0.9874	-0.048	1.9819	0.1401	-0.1316	0.1038	0.1839	-0.0304	0.0272	-0.3509	0.0832	-0.0594	0.2075	-0.0205	0.0523	0.1311	0.0074	0.1109	9.8104	0.8985	71.7576
11	2.921	0.4795	1.1551	1.0385	-1.2913	2.7477	0.0568	-0.0164	-0.4634	-0.1898	0.0535	-0.1764	0.6056	-0.0117	-0.1121	0.2309	0.0693	-0.0008	0.1396	0.0185	0.1182	19.2447	-31.3233	49.3524
12	1.2495	-0.469	0.633	2.5204	-0.1301	1.1233	-0.0487	-0.1972	-0.1369	0.1912	0.084	0.0766	0.257	-0.0965	-0.0187	0.1969	0.0278	-0.0025	0.1461	0.0456	0.1194	17.0984	-25.7775	59.52
13	1.5666	-1.7985	-1.7098	2.0946	1.9632	1.8697	-0.4785	-0.0179	-0.5034	0.4003	-0.1302	0.6667	0.8428	-0.1185	0.1466	0.3436	-0.0343	0.0708	0.1221	0.0191	0.2489	7.0426	-35.3727	54.6921
14	0.6922	-0.2144	0.0961	1.8496	0.1292	2.0052	0.0101	0.0045	-0.0656	-0.1918	-0.0046	0.0642	0.2126	0.0206	0.0006	0.1179	0.0257	-0.0166	0.0831	0.0315	0.0923	12.0626	-20.5995	50.2681
15	1.482	-0.127	-0.4324	1.559	-0.8998	0.7048	0.079	-0.1021	0.1876	0.3439	-0.0624	-0.0125	-0.1092	0.0451	-0.0334	0.1411	-0.0638	0.0101	0.0936	-0.0076	0.1498	18.3506	19.6114	56.06
16	1.213	1.2271	2.1448	1.3462	2.0052	4.0728	-0.1923	-0.0811	0.4473	-0.367	0.0029	0.3938	-0.9421	0.0633	0.1386	0.2943	-0.0108	0.0861	0.0665	-0.0367	0.3179	7.4684	26.873	55.7653

Refinement TLS group

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

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