PDB-9yg7: Crystal structure of Shewanella benthica group 1 truncated hemogl...

ID or keywords:

Entry

Database: PDB / ID: 9yg7

Title

Crystal structure of Shewanella benthica group 1 truncated hemoglobin H24I/C51S/ C71S variant

Components

Group 1 truncated hemoglobin

Keywords

UNKNOWN FUNCTION / TRUNCATED 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: 1.6 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Shewanella benthica group 1 truncated hemoglobin H24I/C51S/ C71S variant
Authors: Schultz, T.D. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.

History

Deposition	Sep 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2026	Group: Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yg7.cif.gz	264.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9yg7.ent.gz	177.1 KB	Display	PDB format
PDBx/mmJSON format	9yg7.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/yg/9yg7 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/9yg7	HTTPS FTP

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Related structure data

Related structure data	7tt9 8tls 8ugz 8uzu
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 (5) #206 - Feb 2017 Globin Evolution similarity (2) #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

#41 - May 2003
Hemoglobin
similarity (5)
#206 - Feb 2017
Globin Evolution
similarity (2)
#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
Evidence: homology

Unit cell

Length a, b, c (Å)	27.593, 104.992, 150.977
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Group 1 truncated hemoglobin Mass: 12813.438 Da / Num. of mol.: 4 / Mutation: H24I, 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-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.: 355 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 mM Protein 10 mM KCN 0.1 M Bis-Tris pH 6.5 27% PEG MME 2000 Temp details: Room temp, subject to fluctuations

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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: May 9, 2025 / Details: NULL
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: 1.6→22.86 Å / Num. obs: 59443 / % possible obs: 99.9 % / Redundancy: 13.2 % / B_iso Wilson estimate: 9.86 Å² / R_merge(I) obs: 0.011 / R_sym value: 0.043 / Net I/σ(I): 88.7
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 9.6 % / R_merge(I) obs: 0.059 / Mean I/σ(I) obs: 16.38 / Num. unique obs: 5947 / R_sym value: 0.117 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
CrysalisPro	43.9	data reduction
CrysalisPro	43.9	data scaling
PHENIX	1.20.1_4487	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.6→22.86 Å / SU ML: 0.1316 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 18.0928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2009	1978	3.36 %
R_work	0.1764	56888	-
obs	0.1772	58866	99.16 %

Solvent computation

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

Displacement parameters

B_iso mean: 11.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→22.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3584	0	180	355	4119

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	4393
X-RAY DIFFRACTION	f_angle_d	0.92	6073
X-RAY DIFFRACTION	f_chiral_restr	0.053	645
X-RAY DIFFRACTION	f_plane_restr	0.0075	787
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0412	1815

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 (%)
1.6-1.64	0.2016	140	0.1493	4006	X-RAY DIFFRACTION	98.86
1.64-1.68	0.1937	136	0.1513	3954	X-RAY DIFFRACTION	99.34
1.68-1.73	0.2116	143	0.1534	4062	X-RAY DIFFRACTION	99.46
1.73-1.79	0.1996	139	0.1573	3944	X-RAY DIFFRACTION	99.37
1.79-1.85	0.1945	140	0.1702	4067	X-RAY DIFFRACTION	99.29
1.85-1.93	0.2486	135	0.1853	3919	X-RAY DIFFRACTION	97.76
1.93-2.02	0.2217	140	0.1806	4012	X-RAY DIFFRACTION	98.58
2.02-2.12	0.1675	141	0.1712	4103	X-RAY DIFFRACTION	99.79
2.12-2.25	0.2044	140	0.1709	3975	X-RAY DIFFRACTION	98.54
2.25-2.43	0.2339	139	0.1848	4019	X-RAY DIFFRACTION	98.23
2.43-2.67	0.1985	143	0.1905	4095	X-RAY DIFFRACTION	99.84
2.67-3.06	0.2264	145	0.2035	4175	X-RAY DIFFRACTION	99.88
3.06-3.85	0.1822	145	0.1817	4162	X-RAY DIFFRACTION	99.63
3.85-22.86	0.1786	152	0.1653	4395	X-RAY DIFFRACTION	99.65

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	1.86086227054	1.65640898776	-0.818610324325	2.0499259431	-1.18195422061	2.44940629491	0.0531349310071	-0.136564100059	0.0137252155211	0.0916611606626	-0.0867880594706	0.0346983550617	0.0133220750811	0.247381970629	0.0291721351424	0.0643760121068	0.00867872805368	-0.0138239261409	0.0569256207744	-0.0099491402967	0.0781418476146	12.2099701873	43.0572939147	45.8495503055
2	0.719231978098	0.461891506837	-0.53680916604	0.572794142805	-0.27121297376	1.9896426281	-0.00933532313468	-0.0493716757625	0.100041275216	0.0252698020482	-0.0167653373512	0.0520581193525	-0.255862200353	0.0736308137568	0.0141717015214	0.0980781031117	-0.00526684941953	-0.0330170140761	0.059414862899	-0.00520362549556	0.0762418162606	9.26051249851	52.931443984	40.8869710435
3	1.05310796752	-0.421674240709	-0.0638303398559	1.5997965732	-0.487227813536	1.92810624688	0.0350752246449	-0.0514957046087	-0.0509953189733	0.109939673361	-0.0921740203122	0.092107326853	-0.310253066485	-0.136995609988	0.0390142011164	0.0682397710755	-0.00112152857729	-0.024399364759	0.0523569068767	-0.0166901118026	0.0695807276749	-1.50360487023	51.9803822412	41.1692971357
4	0.338598751761	0.261091200935	0.168950097303	1.8724195846	-0.255870447035	1.70932027887	0.00102277068248	-0.0207542613889	-0.00506627828722	0.00427830228708	-0.0670361600923	0.00993565845737	0.0260742207008	0.0229594213229	0.0609079728193	0.0429624758245	-0.0010511251607	-0.00167223314834	0.0439907363899	-0.0224066847556	0.0623138802063	6.07020651919	38.9385243219	37.0965483619
5	1.97178131515	-1.55080903592	0.936992814416	1.50292569783	-1.03195293204	1.90347617581	0.0475991546377	0.157602510753	0.0178648114056	-0.0683680381416	-0.022910968345	-0.0259826915629	-0.149180843038	0.159123180039	-0.0413247448034	0.0898879099808	-0.028026440058	0.0359434639292	0.0740782747359	-0.0164286737323	0.0909408240341	10.4049371679	54.7831441287	-7.45001150676
6	0.485763602022	-0.37242918499	-0.5155704482	0.559322012388	1.11013740013	6.42672673555	-0.0521263973592	0.0451567880558	-0.178487193377	-0.00273105442561	0.0816146912342	-0.172973995433	0.286289319906	0.243058935174	-0.0152780328206	0.0520902096508	0.0125308819278	0.023811972288	0.0880201492697	-0.00643787822732	0.0779978533724	11.1896900387	41.3346256746	6.20365926985
7	0.965612870758	0.492088748744	-0.324613831206	1.34884189828	-0.36400181043	1.67402927088	-0.0169076247304	0.109286560716	0.00681491174858	-0.16910047394	0.0581596108597	-0.0267682402066	0.0130904647403	0.0421813259042	-0.0359949646362	0.0568730972379	-0.00200302128987	0.0158448719088	0.0743131048875	-0.00671373532524	0.0608547278489	3.94118260283	48.7073469429	-1.4764921894
8	0.619189994806	-0.522313416686	-0.277196301635	1.25257848424	-0.31491499769	1.75214199245	0.088205348607	0.0783722672739	0.183885620733	-0.0681673073853	0.0197138245208	-0.0414482098553	-0.329317610213	0.00795602277505	-0.087506030851	0.124575019057	-0.000303416421935	0.0179204440617	0.0721550782807	-0.0171029583034	0.0714307328037	2.88697140437	59.3967961361	1.21573541241
9	1.55545693128	-0.359801276705	1.89485003115	0.563175909971	-0.488350902758	2.41864074087	0.219227089687	0.0581168810162	-0.234613726753	-0.0365092820295	-0.0294985159939	0.141164521916	0.307207014304	0.0110487824429	-0.177029799397	0.0794503175784	-0.00788355275932	9.03914405159E-5	0.0976677019686	-0.0142039465962	0.0920511703479	-5.18095178146	20.4585486659	25.9904146313
10	0.404247214192	0.87049512053	0.15350237005	4.55783836989	0.0849848115402	0.180082589086	-0.063510035433	0.183691008786	-0.0147749293903	-0.361343385907	0.066729990923	0.136182270885	-0.0395341472114	-0.00416581155512	0.0129266303243	0.0611980651589	-0.00903560337535	-0.0206414666572	0.0805723680606	-0.0171543332937	0.0727797761071	-6.03506262963	34.0832915932	12.4233561732
11	2.26484329156	-0.889309357359	0.381156080742	1.72659961878	-0.409820423106	3.06851916891	0.0347761188004	0.235907693603	-0.292994942751	-0.0264082705773	-0.0240424198092	0.0739360189279	0.0913063361552	0.231891870637	-0.00403282235263	0.0786683524284	0.00890888475319	-0.00487822975634	0.0800544008902	-0.025645037437	0.0892452911501	-1.21639233789	19.9386379397	17.9288620576
12	1.556815588	0.072636096212	-1.05255046574	0.00326516282877	-0.0494348970542	0.712587457309	-0.333659260144	-0.185736062878	-0.460946538886	-0.299172716459	-0.0484634364628	-0.10395243746	0.791658157889	0.0680566200359	0.149815787392	0.252293354911	0.0235600354111	0.0491993297825	0.0840382173086	0.00273731333919	0.192360018932	7.56993936206	17.4007129731	18.8991049088
13	0.109821381203	0.0191191570512	0.231427554562	1.19599361066	-0.297231455665	0.920926927094	0.0232833169805	-0.0170225780025	0.0111794641067	0.0677711288068	0.0134332758228	0.038756687123	-0.0033392529072	-0.0517207305511	-0.0164825633236	0.0246763470344	-0.00551421751301	-0.00152898776438	0.0514633982672	-0.00750249986633	0.0518649497568	1.72618003868	31.8980513732	25.7453142345
14	1.85079500103	0.695149908042	0.847798354112	0.261340465078	0.318346570531	0.388308293536	0.0956826368674	0.0664283009725	0.293131842778	-0.181245417216	-0.0946481997986	0.0370425732789	-0.406169545429	-0.0542397432954	-0.119001506942	0.42096739191	0.0483413266134	0.0898357051257	0.112419342161	0.0119690669008	0.141879052481	-1.21745212896	80.8376454556	6.79579060796
15	2.41038234882	1.58737216836	-0.652219561348	2.94476333	-1.73607268041	2.30590668581	0.0450999529742	0.00167637844236	0.0942933651207	-0.151545622091	-0.109865167671	0.35450096895	-0.226790286493	-0.0440138638914	0.0484934335662	0.138555385991	0.0514567849111	0.00832261540127	0.0914068970938	-0.0120786288279	0.0810241932188	-9.22904316148	71.5594904808	17.8946615562
16	0.212388555145	-0.0604080686046	-0.00332961845725	0.274016576125	0.0480172922358	0.00841978317617	-0.0359698720215	-0.0987418094405	-0.0524405518148	0.499450810104	0.13359322706	0.00139053738621	0.124316300442	-0.00476035554992	-0.0588907097339	0.186302421048	0.0511788883534	0.012650386903	0.0848650092518	0.00582743687513	0.0798809332165	-6.41579684772	61.6653749057	27.5060851465
17	2.24489084362	0.969156463888	-0.403072481406	2.02178795252	-0.374222706704	2.13781773011	-0.0126463340929	-0.0979619525138	0.152432585019	-0.205088340481	0.0461811245474	-0.0222156523917	-0.0707639045994	0.0796262497367	-0.0450137076411	0.0967031842138	0.014234800962	0.0164059303635	0.0476901465891	-0.011795193914	0.0708214192017	-1.9275003094	75.8597566657	21.7495993612
18	2.96962145891	-0.661728834104	2.01494044883	0.184295737822	-0.257040128898	2.36623363457	-0.205348914088	0.198136789834	0.814459730232	0.0511082500458	0.0218459819142	-0.230440897036	-1.09639379244	-0.0367742151708	0.0978169863363	0.325712703859	0.023780511304	0.0123393787272	0.10289626	-0.00488274419465	0.258204170728	6.03518725938	78.9389602529	21.304591926
19	0.858789290428	0.0698935780983	0.0366122134959	2.06252689305	0.342013119117	0.95615275364	0.0998994439901	0.0881084982229	-0.0437839959803	-0.0218984988697	-0.0199015377123	-0.0465132992206	-0.0238219584693	-0.0412795953903	-0.0784776851979	0.052701720863	0.0268057858074	0.00345078882902	0.0720578990616	-0.0137764967864	0.0509875041755	0.253031355875	62.2632701467	18.6532607538
20	0.421898000842	-0.0425635025461	-0.62122918984	1.57454417326	0.0161924092506	0.91450636362	0.06740882921	0.105346881339	0.13403511034	-0.324754142081	0.00185246116575	-0.0777194268245	-0.271241781908	-0.0772600091159	-0.0875968381415	0.199153839918	0.0415067591688	0.00811778503355	0.119784028811	-0.0242651317248	0.0774101767665	1.44013285241	67.3151833146	9.30188641752

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 2 through 26 )	A	A	2 - 26	1 - 25
2	2	chain 'A' and (resid 27 through 54 )	A	A	27 - 54	26 - 53
3	3	chain 'A' and (resid 55 through 75 )	A	A	55 - 75	54 - 74
4	4	chain 'A' and (resid 76 through 117 )	A	A	76 - 117	75 - 116
5	5	chain 'B' and (resid 2 through 26 )	B	D	2 - 26	1 - 25
6	6	chain 'B' and (resid 27 through 38 )	B	D	27 - 38	26 - 37
7	7	chain 'B' and (resid 39 through 92 )	B	D	39 - 92	38 - 91
8	8	chain 'B' and (resid 93 through 117 )	B	D	93 - 117	92 - 116
9	9	chain 'C' and (resid 2 through 26 )	C	G	2 - 26	1 - 25
10	10	chain 'C' and (resid 27 through 38 )	C	G	27 - 38	26 - 37
11	11	chain 'C' and (resid 39 through 54 )	C	G	39 - 54	38 - 53
12	12	chain 'C' and (resid 55 through 64 )	C	G	55 - 64	54 - 63
13	13	chain 'C' and (resid 65 through 117 )	C	G	65 - 117	64 - 116
14	14	chain 'D' and (resid 2 through 9 )	D	J	2 - 9	1 - 8
15	15	chain 'D' and (resid 10 through 26 )	D	J	10 - 26	9 - 25
16	16	chain 'D' and (resid 27 through 38 )	D	J	27 - 38	26 - 37
17	17	chain 'D' and (resid 39 through 54 )	D	J	39 - 54	38 - 53
18	18	chain 'D' and (resid 55 through 64 )	D	J	55 - 64	54 - 63
19	19	chain 'D' and (resid 65 through 92 )	D	J	65 - 92	64 - 91
20	20	chain 'D' and (resid 93 through 117 )	D	J	93 - 117	92 - 116

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Feb 9, 2022. New format data for meta-information of EMDB entries

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