PDB-2r1h: met-Trout IV hemoglobin at pH 6.3

ID or keywords:

Entry

Database: PDB / ID: 2r1h

Title

met-Trout IV hemoglobin at pH 6.3

Components

Hemoglobin subunit alpha-4
Hemoglobin subunit beta-4

Keywords

OXYGEN BINDING / trout hemoglobin / autoxidation / hemin loss / heme pocket / Iron / Metal-binding / Oxygen transport / Transport

Function / homology

Function and homology information

haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / heme binding / metal ion binding
Similarity search - Function

Biological species

Oncorhynchus mykiss (rainbow trout)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Aranda IV, R. / Worley, C.E. / Richards, M.P. / Phillips Jr., G.N.

Citation

Journal: Proteins / Year: 2008
Title: Structural analysis of fish versus mammalian hemoglobins: Effect of the heme pocket environment on autooxidation and hemin loss.
Authors: Aranda, R. / Cai, H. / Worley, C.E. / Levin, E.J. / Li, R. / Olson, J.S. / Phillips Jr., G.N. / Richards, M.P.

History

Deposition	Aug 22, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 30, 2013	Group: Database references / Structure summary

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r1h.cif.gz	134.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2r1h.ent.gz	114.4 KB	Display	PDB format
PDBx/mmJSON format	2r1h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2r1h_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	2r1h_full_validation.pdf.gz	1.8 MB	Display
Data in XML	2r1h_validation.xml.gz	28.7 KB	Display
Data in CIF	2r1h_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r1/2r1h ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r1h	HTTPS FTP

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Related structure data

Related structure data	2qspC 2qssC 3bj1C 3bj2C 3bj3C C: citing same article (ref.)
Similar structure data	1y0t-d 2peg-1 3bom-d 3gkv-1 6ka9-2 6lcw-1 3cy5-d 3gqg-d 1v4w-d 1y22-d Search similar-shape structures by Omokage search (details) 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	#41 - May 2003 Hemoglobin similarity (3) #206 - Feb 2017 Globin Evolution similarity (3) #257 - May 2021 Fetal Hemoglobin similarity (3) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (3) #159 - Mar 2013 Erythrocruorin similarity (3) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#41 - May 2003
Hemoglobin
similarity (3)
#206 - Feb 2017
Globin Evolution
similarity (3)
#257 - May 2021
Fetal Hemoglobin
similarity (3)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (3)
#159 - Mar 2013
Erythrocruorin
similarity (3)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (3)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (3)
#142 - Oct 2011
PDB Pioneers
similarity (3)

Deposited unit

A: Hemoglobin subunit alpha-4

B: Hemoglobin subunit beta-4

C: Hemoglobin subunit alpha-4

D: Hemoglobin subunit beta-4

hetero molecules

66.6 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)	57.063, 62.998, 77.016
Angle α, β, γ (deg.)	90.000, 92.200, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hemoglobin subunit alpha-4 / Hemoglobin alpha-4 chain / Alpha-4- globin Mass: 15851.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus mykiss (rainbow trout) / References: UniProt: P14527
#2: Protein	Hemoglobin subunit beta-4 / Hemoglobin beta-4 chain / Beta-4-globin / Hemoglobin beta-IV chain Mass: 16038.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus mykiss (rainbow trout) / References: UniProt: P02141
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 20% PEG 4K, 0.1 M BisTris , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97893 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97893 Å / Relative weight: 1
Reflection	Resolution: 1.9→76.9 Å / Num. obs: 42904

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3	data extraction
HKL-2000		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Resolution: 1.9→76.92 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.94 / SU B: 6.917 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	2132	5 %	RANDOM
R_work	0.17	-	-	-
obs	0.172	42596	98.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.883 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4 Å²	0 Å²	-0.91 Å²
2-	-	-2.1 Å²	0 Å²
3-	-	-	1.63 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→76.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4496	0	192	352	5040

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	4933
X-RAY DIFFRACTION	r_angle_refined_deg	1.408	2.064	6773
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.095	5	605
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.851	24.184	196
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.243	15	807
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.415	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	743
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3704
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	2675
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3421
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	347
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.179	0.2	33
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.139	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.728	1.5	3028
X-RAY DIFFRACTION	r_mcangle_it	1.043	2	4770
X-RAY DIFFRACTION	r_scbond_it	1.866	3	2189
X-RAY DIFFRACTION	r_scangle_it	2.691	4.5	1978

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	126	-
R_work	0.218	2673	-
all	-	2799	-
obs	-	-	87.99 %

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	6.2371	-5.6768	-1.4266	10.8655	0.6733	0.9244	-0.1902	-0.6217	-0.2193	1.1496	0.3473	0.5733	-0.0788	0.0603	-0.1572	0.3215	0.0484	0.0714	0.0604	0.0411	-0.1711	8.9412	-1.2406	40.7044
2	3.5067	-1.4376	0.41	2.015	0.0435	4.6516	-0.0108	0.1739	-0.068	0.1914	-0.0053	-0.3906	0.0183	0.2644	0.0162	0.0228	-0.0034	-0.0602	0.0856	0.0164	0.0707	19.8426	-4.3185	23.9476
3	2.0147	-0.4453	-1.3676	2.9456	-0.1149	2.8898	-0.0663	-0.1663	-0.0224	0.4974	-0.0028	-0.587	0.1452	0.2408	0.0692	0.0719	0.0229	-0.1306	0.0738	0.0149	0.0392	25.3896	-2.9367	31.7061
4	14.4429	2.0602	-7.8703	5.0836	-1.9126	9.1411	0.1492	-0.5583	0.2864	1.0245	-0.168	-0.321	-0.7483	0.3544	0.0188	0.2775	-0.0227	-0.2077	-0.07	-0.0516	-0.0711	22.3233	11.5243	39.0238
5	1.6454	0.7017	0.0058	3.8239	-0.4888	0.8221	-0.073	-0.0437	-0.0074	0.6342	0.1038	-0.0041	-0.0496	-0.0709	-0.0308	0.1514	0.0228	0.0095	0.0879	0.0186	-0.0378	12.2975	1.2567	30.3609
6	5.2454	3.4688	-2.182	5.5718	-2.3982	1.709	0.0499	-0.1408	0.2682	1.0933	-0.0008	-0.0388	-0.5198	-0.0241	-0.0491	0.2107	-0.0006	-0.1028	0.031	-0.0393	-0.0143	19.0781	13.6792	32.941
7	25.2659	-16.4237	0.1552	31.0702	7.0173	23.0507	0.8287	1.8937	1.1883	-1.3476	-1.0788	-0.9653	-0.1462	0.998	0.2501	0.0201	0.078	0.0526	0.1001	0.0854	-0.0922	15.5392	-8.6136	5.0103
8	0.6397	-1.3459	0.4805	2.9958	-0.6377	1.2116	0.016	-0.0528	-0.1892	0.0356	0.2103	0.6172	0.0882	-0.2317	-0.2263	-0.024	-0.0363	0.0229	0.0731	0.0565	0.1482	-1.0427	-2.5131	19.0094
9	6.6156	-0.4314	-0.7842	3.8706	-5.5135	8.1516	0.1867	-0.6847	-0.6055	0.5513	0.605	0.9497	-0.6308	-0.9154	-0.7917	-0.0449	0.0787	0.1371	0.2865	0.2552	0.4624	-12.2656	1.5099	25.4145
10	17.3833	-5.6084	-15.834	4.189	3.4554	20.584	-0.2624	0.5461	-0.442	-0.5013	0.1628	1.1902	0.8379	-0.6383	0.0996	0.0116	-0.0728	-0.1722	-0.0433	0.0141	0.2083	-1.4039	-6.5969	8.4628
11	6.5854	-7.4072	-4.8172	14.7579	7.9407	6.6075	0.082	0.0804	-0.1484	-0.6495	-0.1419	0.67	-0.0585	-0.1062	0.06	0.1041	-0.0012	-0.1659	0.0317	0.0363	0.0123	-0.6748	4.6005	3.2545
12	0.9897	-1.1512	0.5785	4.4054	-0.6684	0.8602	0.0792	0.06	-0.0752	-0.2109	-0.0322	0.2517	0.0754	-0.0008	-0.0469	0.0333	-0.0144	-0.0276	0.0899	0.0014	0.0409	6.0549	-0.0086	15.0777
13	5.7825	-4.4503	4.558	8.6745	-9.4472	20.5351	-0.1831	-0.5617	0.6027	0.3484	0.3374	-0.0502	0.4198	-0.1055	-0.1544	0.0901	0.0245	-0.2625	-0.0289	-0.1014	0.1491	21.5617	31.8149	30.7208
14	1.569	-0.6769	0.9332	6.7137	1.9773	2.5852	0.045	0.0733	0.1127	-0.1385	-0.0765	-0.34	-0.1395	-0.1049	0.0315	0.0184	0.0028	0.0342	0.0891	0.0065	0.031	9.6866	32.7306	14.1549
15	1.6857	-0.3654	1.0072	4.6783	-0.2225	1.4165	-0.1098	0.0025	0.0634	0.0605	0.0727	0.4477	-0.0964	-0.0663	0.0371	0.0068	0.0097	0.0277	0.1121	0.0038	0.0423	1.2791	29.7586	16.6284
16	5.4452	4.4402	3.6311	12.6601	2.8352	4.2032	0.1052	-0.5105	0.3197	1.8274	-0.0708	0.7042	-0.0624	-0.1402	-0.0343	0.2677	0.0324	0.1732	0.0607	0.0136	-0.1139	2.788	24.2464	30.69
17	1.8772	-0.2026	-0.149	4.9252	-0.0688	0.9319	-0.0498	0.0078	0.1395	0.2177	0.0305	-0.7614	-0.0378	-0.0195	0.0192	-0.0035	0.0082	-0.043	0.0509	-0.0172	0.1074	17.3934	28.1694	18.99
18	3.9858	2.4796	-1.0366	12.4837	-1.3532	1.8169	0.052	-0.0791	-0.1666	1.7741	-0.0018	-0.0445	-0.3967	-0.0417	-0.0502	0.2823	0.0619	0.0081	0.065	0.002	-0.1347	7.1535	19.2064	30.0738
19	9.5315	0.7335	1.4303	10.6372	2.018	2.2831	0.4025	0.431	-0.1082	-1.4906	-0.3997	-0.4688	-0.0064	-0.0388	-0.0029	0.3604	0.1312	0.17	0.0592	0.0383	-0.0951	16.9159	20.4536	-4.2753
20	2.1943	-2.8707	-0.193	3.806	0.5567	1.8588	-0.1511	0.0316	0.6705	0.0838	0.0325	-1.405	-0.0583	0.1536	0.1185	-0.1489	-0.0168	0.0149	-0.0236	0.0236	0.4694	31.9716	19.8999	15.6502
21	7.5878	3.1554	5.0485	7.2247	3.463	6.5095	0.2692	-0.1315	0.229	-0.0625	-0.2574	-1.965	0.2633	0.4131	-0.0118	0.0799	0.0455	0.2156	0.0448	0.1325	0.6855	34.2152	19.8846	8.6301
22	2.4464	-0.4085	1.3125	2.8101	2.1138	6.7109	0.0578	0.1179	-0.1413	-0.3447	-0.1136	-0.4749	0.0735	0.2964	0.0559	-0.0157	0.0206	0.1333	0.0002	0.0238	0.1797	28.2351	5.5705	7.6528
23	1.6467	-1.8005	0.4936	5.7024	0.1008	0.7175	0.1517	0.1414	0.1385	-0.638	-0.1806	-0.6098	0.0277	0.0684	0.0289	0.0272	0.0176	0.156	0.0696	0.0378	0.0767	19.2291	21.5889	6.6597
24	3.9409	3.0985	-3.1321	8.3056	-8.5425	11.0432	0.2493	0.8262	-0.8397	-0.9434	0.3804	-0.119	0.9409	-0.622	-0.6297	0.1454	0.0268	0.0077	0.0325	-0.0454	0.207	24.4601	-0.3264	9.6028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 23	2 - 24
2	X-RAY DIFFRACTION	2	A	A	24 - 39	25 - 40
3	X-RAY DIFFRACTION	3	A	A	40 - 73	41 - 74
4	X-RAY DIFFRACTION	4	A	A	74 - 90	75 - 91
5	X-RAY DIFFRACTION	5	A	A	91 - 130	92 - 131
6	X-RAY DIFFRACTION	6	A	A	131 - 142	132 - 143
7	X-RAY DIFFRACTION	7	B	B	1 - 6	1 - 6
8	X-RAY DIFFRACTION	8	B	B	7 - 44	7 - 44
9	X-RAY DIFFRACTION	9	B	B	45 - 64	45 - 64
10	X-RAY DIFFRACTION	10	B	B	65 - 78	65 - 78
11	X-RAY DIFFRACTION	11	B	B	79 - 95	79 - 95
12	X-RAY DIFFRACTION	12	B	B	96 - 147	96 - 147
13	X-RAY DIFFRACTION	13	C	C	1 - 13	2 - 14
14	X-RAY DIFFRACTION	14	C	C	14 - 37	15 - 38
15	X-RAY DIFFRACTION	15	C	C	38 - 72	39 - 73
16	X-RAY DIFFRACTION	16	C	C	73 - 95	74 - 96
17	X-RAY DIFFRACTION	17	C	C	96 - 130	97 - 131
18	X-RAY DIFFRACTION	18	C	C	131 - 142	132 - 143
19	X-RAY DIFFRACTION	19	D	D	1 - 18	1 - 18
20	X-RAY DIFFRACTION	20	D	D	19 - 44	19 - 44
21	X-RAY DIFFRACTION	21	D	D	45 - 78	45 - 78
22	X-RAY DIFFRACTION	22	D	D	79 - 102	79 - 102
23	X-RAY DIFFRACTION	23	D	D	103 - 142	103 - 142
24	X-RAY DIFFRACTION	24	D	D	143 - 147	143 - 147

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Yorodumi