PDB-12rm: Structure of turkey hemoglobin A at 1.7 Angstrom resolution (tetr...

ID or keywords:

Entry

Database: PDB / ID: 12rm

Title

Structure of turkey hemoglobin A at 1.7 Angstrom resolution (tetragonal form)

Components

Hemoglobin beta chain
Hemoglobin subunit alpha-A

Keywords

OXYGEN TRANSPORT / Caffeic acid / anti-oxidant

Function / homology

Function and homology information

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

Biological species

Meleagris gallopavo (turkey)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.695 Å

Authors

Bingman, C.A. / Yin, J. / Smith, R.W. / Richards, M.P.

Funding support

United States, 1items

Citation

Journal: J.Agric.Food Chem. / Year: 2026
Title: Oxidative Characteristics of Turkey Hemoglobin A Containing Covalently Bound Epigallocatechin Gallate.
Authors: Yin, J. / Zhang, W. / Tatiyaborworntham, N. / Bingman, C.A. / Richards, M.P.

History

Deposition	Apr 15, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	12rm.cif.gz	229.1 KB	Display	PDBx/mmCIF format
PDB format	pdb12rm.ent.gz	154.1 KB	Display	PDB format
PDBx/mmJSON format	12rm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2r/12rm ftp://data.pdbj.org/pub/pdb/validation_reports/2r/12rm	HTTPS FTP

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Related structure data

Related structure data	12rhC 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	#41 - May 2003 Hemoglobin similarity (4) #206 - Feb 2017 Globin Evolution similarity (4) #257 - May 2021 Fetal Hemoglobin similarity (4) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (4) #159 - Mar 2013 Erythrocruorin similarity (4) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (4) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (4) #142 - Oct 2011 PDB Pioneers similarity (4)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#41 - May 2003
Hemoglobin
similarity (4)
#206 - Feb 2017
Globin Evolution
similarity (4)
#257 - May 2021
Fetal Hemoglobin
similarity (4)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (4)
#159 - Mar 2013
Erythrocruorin
similarity (4)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (4)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (4)
#142 - Oct 2011
PDB Pioneers
similarity (4)

Deposited unit

A: Hemoglobin subunit alpha-A

B: Hemoglobin beta chain

hetero molecules

32.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemoglobin subunit alpha-A

B: Hemoglobin beta chain

hetero molecules

A: Hemoglobin subunit alpha-A

B: Hemoglobin beta chain

hetero molecules

defined by author
Evidence: gel filtration
65 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.310, 81.310, 106.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2
Space group name Hall	P4n2n
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/2 #3: y+1/2,-x+1/2,z+1/2 #4: x+1/2,-y+1/2,-z+1/2 #5: -x+1/2,y+1/2,-z+1/2 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-445- HOH
2	1	A-475- HOH
3	1	B-458- HOH

#1: Protein	Hemoglobin subunit alpha-A / Alpha-A-globin / Hemoglobin alpha-A chain Mass: 14913.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: G1N9H8
#2: Protein	Hemoglobin beta chain Mass: 16329.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P84479
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.83 Å³/Da / Density % sol: 56.48 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 200 nL protein at 18.7 mg/mL, 10 mM Tris pH 8.0 was mixed with 200 nL reservoir solution 16 % PEG 3350, 0.2 M sodium citrate. Vapor diffusion in MRC plate. Crystal was cryoprotected by ...Details: 200 nL protein at 18.7 mg/mL, 10 mM Tris pH 8.0 was mixed with 200 nL reservoir solution 16 % PEG 3350, 0.2 M sodium citrate. Vapor diffusion in MRC plate. Crystal was cryoprotected by soaking in a solution made by supplementing 16 microliters of reservoir with 2.3 mg solid PEG 3350. Crystals were quenched by looping and direct immersion in liquid nitrogen

Crystal

Density Matthews: 2.83 Å³/Da / Density % sol: 56.48 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200 nL protein at 18.7 mg/mL, 10 mM Tris pH 8.0 was mixed with 200 nL reservoir solution 16 % PEG 3350, 0.2 M sodium citrate. Vapor diffusion in MRC plate. Crystal was cryoprotected by ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.97934 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 1.695→44.65 Å / Num. obs: 40382 / % possible obs: 99.9 % / Redundancy: 11.8 % / B_iso Wilson estimate: 27.78 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.121 / R_rim(I) all: 0.127 / Net I/σ(I): 12.79

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.7-1.74	2.941	2909	0.44	3.073	1
1.74-1.79	2.283	2877	0.546	2.385	1
1.79-1.84	1.828	2766	0.682	1.911	1
1.84-1.9	1.859	2731	0.806	1.943	1
1.9-1.96	0.931	2611	0.871	0.974	1
1.96-2.03	0.74	2558	0.931	0.774	1
2.03-2.1	0.504	2443	0.962	0.527	1
2.1-2.19	0.386	2385	0.975	0.403	1
2.19-2.29	0.36	2264	0.98	0.378	1
2.29-2.4	0.239	2211	0.989	0.25	1
2.4-2.53	0.174	2062	0.993	0.183	1
2.53-2.68	0.143	1985	0.994	0.15	1
2.68-2.87	0.111	1867	0.995	0.116	1
2.87-3.09	0.087	1742	0.997	0.092	1
3.09-3.39	0.076	1624	0.997	0.079	1
3.39-3.79	0.066	1462	0.998	0.069	1
3.79-4.38	0.055	1319	0.998	0.057	1
4.38-5.36	0.05	1131	0.999	0.053	1
5.36-7.58	0.048	897	0.999	0.05	1
7.58-44.65	0.043	538	0.999	0.046	1

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XSCALE	VERSION Jan 10, 2022 BUILT=20220220	data scaling
XDS	VERSION Jan 10, 2022 BUILT=20220220	data reduction
PDB_EXTRACT		data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.695→44.65 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2169	2656	6.58 %
R_work	0.1837	37738	-
obs	0.186	40382	99.85 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.695→44.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2205	0	88	374	2667

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	2401
X-RAY DIFFRACTION	f_angle_d	0.9524	3298
X-RAY DIFFRACTION	f_chiral_restr	0.0428	364
X-RAY DIFFRACTION	f_plane_restr	0.0111	445
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5632	899

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 (%)
1.695-1.73	0.2843	134	0.2797	1910	X-RAY DIFFRACTION	98.51
1.73-1.76	0.2964	137	0.2604	1944	X-RAY DIFFRACTION	100
1.76-1.79	0.2645	137	0.2554	1951	X-RAY DIFFRACTION	100
1.79-1.83	0.2812	139	0.2531	1959	X-RAY DIFFRACTION	100
1.83-1.88	0.275	137	0.2598	1964	X-RAY DIFFRACTION	100
1.88-1.92	0.3955	137	0.349	1948	X-RAY DIFFRACTION	99.81
1.92-1.98	0.3446	139	0.2693	1980	X-RAY DIFFRACTION	99.91
1.98-2.03	0.2607	138	0.2009	1961	X-RAY DIFFRACTION	100
2.03-2.1	0.2259	138	0.1858	1954	X-RAY DIFFRACTION	100
2.1-2.17	0.2343	137	0.178	1964	X-RAY DIFFRACTION	100
2.17-2.26	0.2498	141	0.2154	1985	X-RAY DIFFRACTION	99.81
2.26-2.36	0.1976	139	0.1789	1973	X-RAY DIFFRACTION	99.86
2.36-2.49	0.222	139	0.1661	1989	X-RAY DIFFRACTION	100
2.49-2.64	0.2235	140	0.1629	1983	X-RAY DIFFRACTION	100
2.64-2.85	0.2107	140	0.168	1999	X-RAY DIFFRACTION	100
2.85-3.13	0.1948	143	0.1734	2016	X-RAY DIFFRACTION	99.91
3.14-3.59	0.1965	142	0.1693	2022	X-RAY DIFFRACTION	99.95
3.59-4.52	0.1991	144	0.1488	2062	X-RAY DIFFRACTION	99.82
4.52-44.65	0.1804	155	0.1793	2174	X-RAY DIFFRACTION	99.7

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	0.889046486858	0.925554315877	-0.264330363395	1.12323663284	-0.0638737127338	0.978334512915	0.262588543434	-0.702341223446	-0.189585219915	0.595267123103	-0.194438876229	-0.197528002204	-0.211979602435	0.0968522988069	0.00199056539424	0.387330852597	-0.0316812241021	0.0167283592354	0.419483287145	-0.0710525845363	0.287833519117	-10.6735357739	54.7908292827	-4.61941293818
2	2.24137854418	0.676781591504	0.791699891097	1.55490862601	-1.2147893696	1.92155277674	0.0374667842557	-0.144338685503	0.123818741195	-0.107712998148	-0.0322267171038	0.284255953946	-0.162993814975	-0.210924721816	-5.59115329823E-5	0.165217524069	-0.00458945090999	0.0136055601994	0.317949274657	-0.012149727289	0.249103794215	-21.0404446416	44.3800510091	-20.5753722656
3	1.21131716663	0.749104008928	-0.171839617539	3.36077551697	0.894154994258	0.381962964611	0.0593560626551	-0.16356548431	-0.0634963548795	-0.0258014330421	-0.0524593611399	0.479053699962	-0.156839935023	-0.465244312465	0.000527512358627	0.213800882654	0.0131980033451	0.0427807462618	0.332961804513	-0.024257609001	0.347098888151	-24.0822087181	40.7793486266	-13.8427691861
4	0.0747573567668	-0.0160436746298	0.0222872469784	0.109378680943	-0.144371212849	0.161782144984	0.320170506143	-0.408080590936	0.163880655033	0.352469618127	-0.542003097696	0.579262247184	0.205446446792	0.0613776245297	0.000297613636488	0.311659669835	-0.0317151861294	0.023547576781	0.399499517701	-0.0250939438562	0.285652159652	-10.2516871961	42.2611422546	0.0373495320855
5	0.46624164751	-0.189184061824	-0.175600168577	0.645619589803	0.0559702835299	0.373661009637	-0.136736733836	-0.205017024174	-0.554001037534	0.252269952161	-0.184414483769	-0.144299230853	0.527582924074	0.0125440170461	-1.75097547824E-5	0.280461534007	-0.0161999097724	0.0285002392086	0.323686037511	0.0198285537272	0.316740883805	-13.2059645235	30.5333669648	-10.3949422638
6	0.524263703617	0.654258319168	-0.233368066329	0.84756921977	-0.205712148716	1.15858496918	-0.0413179970226	-0.0128351794827	0.0515882140453	0.106337149743	0.000264618767926	-0.00783331822334	0.00801058394829	0.0439210736254	8.70303105216E-6	0.222364114768	0.00100609733948	0.00226047269866	0.28864779109	-0.019853659845	0.251245805845	-13.9014930401	47.8330148506	-18.675193669
7	1.60582458613	0.541553269406	0.695240706309	0.491645780469	-0.378042509688	1.67886573558	0.0172782699824	-0.115475218219	0.132320272227	0.0460903003377	-0.19738266541	-0.249236113672	0.0475694374313	-0.000991233541381	5.78008837814E-5	0.23838089327	-0.00679047134701	0.0326888644147	0.300634140512	-0.0220780385212	0.231223231832	-8.85469382372	50.8857697153	-11.7906447206
8	1.07646344367	-0.0960761605909	0.143195888454	0.504393800591	-0.345844959716	0.406695919588	0.0915979913457	0.626148271443	-0.155082000351	-0.246644717446	0.124625553945	0.23101488933	0.30232900525	-0.125755305406	-0.000110444473172	0.360932330792	0.0249829011301	-0.0976522957236	0.407228061377	-0.00516349227276	0.401981129509	-16.1301780671	54.8544860944	-38.6936310734
9	0.87914906208	0.0062261987064	-0.545320972244	1.7051637936	-1.35959052008	2.00597765342	0.0104458056735	-0.306154745367	0.266895218242	0.171213427632	-0.00767492227896	-0.196815554738	-0.123822141941	0.0747455680939	-2.79914136901E-5	0.235985677073	0.00412614854026	-0.019685495796	0.28752969451	-0.0315110208595	0.294955473853	2.42517455219	61.6065454529	-20.7971457875
10	1.28759543753	-0.209816925694	-0.600492993913	1.09982984421	-0.131067954134	0.706636181598	-0.0422554512666	0.323636851495	0.411752074453	-0.182902585846	-0.0502515602309	0.089676102506	-0.220890754488	-0.0665629361745	3.76434690453E-5	0.22220757922	0.0272192585988	0.00852375063237	0.285917461126	0.0253236088196	0.297911521481	-1.96086454684	63.3268624663	-33.2436914764
11	0.390299321122	0.0469264228736	-0.443012069313	1.04599944542	0.30461680127	1.26938805523	0.181776903021	0.501220492474	-0.238233010077	-0.543456670751	-0.177292348646	-0.0627223425193	0.282041850902	0.135401760494	4.26652615741E-5	0.390106712712	0.022890767368	0.0149659704617	0.352879379995	0.00303552299768	0.258754710497	2.48971210262	52.3518368637	-41.6907798915
12	1.54280046364	-0.185835340796	0.123333690644	1.91780790991	-0.426812493912	1.39933467106	0.137940304182	0.0327426826218	-0.0953566657163	-0.171976617135	-0.138793997609	0.0281482984139	-0.0586711864035	0.0525439798342	-1.61802376084E-8	0.210626172869	0.00962473539557	-0.010199948813	0.237854163945	0.000403045963978	0.213748600996	-5.65117651464	54.1729930183	-26.7091059326
13	1.14326195405	0.521349938222	0.798758392963	1.42242270904	0.791035496881	1.53238863968	-0.0214775594844	0.208795477312	-0.481632232109	-0.109020798488	-0.0575070630587	-0.00421794739774	0.088497509585	0.112995624418	9.03608447357E-5	0.228960444248	0.0101215109607	-0.00489416806725	0.258824903191	0.0175150592584	0.238992270316	-7.91452215406	49.0153010925	-33.8720974684
14	0.0912208548719	-0.0684119655303	0.0482673934147	0.0763245157003	0.0273564338118	0.120320706838	0.0788190959584	0.126234883864	-0.266242990881	0.323567018035	-0.0368059745203	-0.0548367279162	0.193208813544	-0.53464176168	3.0196670192E-5	0.252993806215	-0.0362543534785	0.035549438193	0.318799828913	-0.0342789818249	0.273813333401	-18.6179486511	36.4184461831	-13.2926843283
15	0.169557161642	-0.169421687764	-0.000987997094644	0.191467675216	0.0990342206534	0.220092091036	-0.23490447739	0.449358680923	0.0192064950717	-0.405851852026	0.274888064536	-0.32602645143	-0.528628720279	0.0675464448899	-7.66744263293E-5	0.310495105273	-0.0066082258996	-0.00913154517641	0.299122811504	0.0135248868664	0.254214465939	4.76066083191	58.1014853359	-31.8106596946

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 17 )	A	A	1 - 17	1 - 17
2	2	chain 'A' and (resid 18 through 42 )	A	A	18 - 42	18 - 42
3	3	chain 'A' and (resid 43 through 71 )	A	A	43 - 71	43 - 71
4	4	chain 'A' and (resid 72 through 80 )	A	A	72 - 80	72 - 80
5	5	chain 'A' and (resid 81 through 94 )	A	A	81 - 94	81 - 94
6	6	chain 'A' and (resid 95 through 112 )	A	A	95 - 112	95 - 112
7	7	chain 'A' and (resid 113 through 138 )	A	A	113 - 138	113 - 138
8	8	chain 'B' and (resid 1 through 19 )	B	D	1 - 19	1 - 19
9	9	chain 'B' and (resid 20 through 57 )	B	D	20 - 57	20 - 57
10	10	chain 'B' and (resid 58 through 76 )	B	D	58 - 76	58 - 76
11	11	chain 'B' and (resid 77 through 94 )	B	D	77 - 94	77 - 94
12	12	chain 'B' and (resid 95 through 121 )	B	D	95 - 121	95 - 121
13	13	chain 'B' and (resid 122 through 146 )	B	D	122 - 146	122 - 146
14	14	chain 'A' and resid 201	A	B	201
15	15	chain 'B' and resid 201	B	E	201

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