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

ID or keywords:

Entry

Database: PDB / ID: 8ugz

Title

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

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 /

SAD / Resolution: 1.8 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.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	Oct 6, 2023	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

-
Download

PDBx/mmCIF format	8ugz.cif.gz	203 KB	Display	PDBx/mmCIF format
PDB format	pdb8ugz.ent.gz	163.5 KB	Display	PDB format
PDBx/mmJSON format	8ugz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8vshC 8w3aC 7tt9 8tls C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

53.9 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)	27.486, 105.058, 151.118
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 Details: First residue of reference sequence A9DF82 (Met) is cleaved by E. coli; first residue of sample (Ser) is numbered 2. 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.: 415 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 42.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23% PEG MME 2000, 100mM Bis-Tris pH 5.5, 10mM KCN, Excluded from light PH range: 5.5-6.5 / Temp details: Room Temp

-
Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
Detector	Type: AGILENT ATLAS CCD / Detector: CCD / Date: Aug 31, 2022 / Details: NULL
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.8→24.33 Å / Num. obs: 41957 / % possible obs: 99.9 % / Redundancy: 5.1 % / R_merge(I) obs: 0.025 / R_sym value: 0.044 / Net I/σ(I): 36.82
Reflection shell	Resolution: 1.8→1.87 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.11 / Mean I/σ(I) obs: 8.08 / Num. unique obs: 4202 / R_sym value: 0.125 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
CrysalisPro	1.171.42.49	data scaling
PHASER	(1.20.1_4487: ???)	phasing
CrysalisPro	1.171.42.49	data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.8→23.29 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 19.48 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2103	1970	4.77 %
R_work	0.1762	-	-
obs	0.1778	41266	98.48 %

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→23.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3592	0	180	415	4187

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4060
X-RAY DIFFRACTION	f_angle_d	0.95	5575
X-RAY DIFFRACTION	f_dihedral_angle_d	12.314	614
X-RAY DIFFRACTION	f_chiral_restr	0.054	593
X-RAY DIFFRACTION	f_plane_restr	0.007	721

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 (%)
1.8-1.85	0.236	140	0.1804	2756	X-RAY DIFFRACTION	97
1.85-1.89	0.2389	130	0.1802	2591	X-RAY DIFFRACTION	95
1.89-1.95	0.2224	142	0.1742	2796	X-RAY DIFFRACTION	99
1.95-2.01	0.2134	135	0.1687	2710	X-RAY DIFFRACTION	98
2.01-2.09	0.1951	141	0.1703	2816	X-RAY DIFFRACTION	100
2.09-2.17	0.1986	140	0.1684	2776	X-RAY DIFFRACTION	99
2.17-2.27	0.202	137	0.1769	2756	X-RAY DIFFRACTION	97
2.27-2.39	0.2241	136	0.1798	2709	X-RAY DIFFRACTION	97
2.39-2.54	0.244	143	0.1759	2851	X-RAY DIFFRACTION	100
2.54-2.73	0.2732	143	0.186	2840	X-RAY DIFFRACTION	100
2.73-3.01	0.2405	142	0.1911	2850	X-RAY DIFFRACTION	100
3.01-3.44	0.1754	145	0.1849	2886	X-RAY DIFFRACTION	99
3.44-4.33	0.1756	143	0.1528	2878	X-RAY DIFFRACTION	99
4.33-23.29	0.196	153	0.1827	3081	X-RAY DIFFRACTION	100

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	0.0337	-0.0577	0.0528	0.1106	-0.092	0.0839	-0.0354	0.0099	0.0088	0.0452	-0.0098	0.0126	-0.008	-0.0585	-0.0177	0.0339	-0.0106	0.0128	0.0585	-0.0104	0.0491	2.2458	62.4128	122.4736
2	-0.0003	0.0013	0.002	0.0559	0.0647	0.0759	-0.0037	0.0006	-0.0153	0.0406	-0.0015	0.0038	0.0913	0.0082	0.0049	0.0452	-0.0113	0.0134	0.0336	-0.0002	0.0175	9.5737	52.9911	117.0137
3	0.0188	0.0039	0.0021	0.0126	0.0206	0.0342	-0.0013	0.0013	0.0125	-0.006	-0.0241	-0.0059	0.0112	0.006	-0.0161	0.0101	-0.0047	0.0089	0.0289	0.0226	0.045	4.2595	63.0296	109.7809
4	0.0395	0.0083	-0.0072	0.0273	0.0094	0.049	-0.0199	-0.0035	-0.0109	0.0102	-0.0253	-0.02	-0.0256	0.0161	-0.0903	0.0486	-0.0079	0.0102	-0.0028	0.0201	0.0821	10.3722	67.8208	114.6888
5	0.0165	0.0023	0.0106	0.0072	0.0013	0.0059	0.0105	-0.0226	-0.0073	-0.0149	0.0153	0.0125	0.0313	-0.031	0.0533	0.0535	-0.0069	-0.0579	0.0601	0.0026	0.0508	2.9391	50.4824	68.7987
6	0.0157	0.0156	-0.0026	0.016	-0.0047	0.0265	-0.0072	-0.0095	0.0118	-0.0039	-0.0129	-0.0014	-0.014	-0.0084	-0.0177	0.019	0.0393	-0.0286	0.0659	-0.0123	0.0512	2.5053	63.7233	81.9025
7	0.0067	0.0018	-0.0042	0.0117	-0.0082	0.009	0.0068	0.0333	0.0178	-0.0118	0.0238	0.0158	-0.0002	-0.0215	0.049	0.0424	0.007	0.0031	0.0948	0.0242	0.0479	7.5244	57.7286	67.29
8	0.0008	0.001	-0.0008	0.0015	0	0.0051	-0.0136	0.0116	-0.0094	-0.0119	-0.0004	0.003	0.0058	-0.01	-0.0051	0.1027	-0.0268	0.0061	0.0927	-0.0068	0.0253	15.3988	56.9075	64.36
9	0.15	-0.0817	-0.0246	0.0583	-0.0371	0.1821	0.027	0.0039	0.0193	-0.0369	0.0173	0.0025	0.0904	0.002	0.058	0.0332	-0.0122	-0.0218	0.0306	0.0142	0.0301	10.0086	51.2382	79.1067
10	0.01	-0.0001	0.0003	0.0064	0.0061	0.0194	0.0118	0.036	-0.0027	0.051	0.0123	-0.0068	-0.0731	0.0098	0.0006	0.0695	-0.0223	0.0033	0.059	0.0162	0.0611	19.2401	83.6837	101.4737
11	0.0043	0.0003	0.0083	0.0022	0.0005	0.0198	-0.007	0.0335	0.019	-0.0094	0.0116	0.0007	-0.0261	-0.0043	-0.0223	0.0381	-0.0138	0.0296	0.0576	0.0344	0.0591	16.8366	78.6236	91.7814
12	0.0029	0.0008	0.0034	0.0004	0.0014	0.0046	-0.0108	-0.0075	0.0068	-0.0004	0.0017	0.0025	-0.0125	0.0012	0.0021	0.0997	0.0216	-0.0221	0.054	0.0109	0.073	6.3927	88.0624	95.1054
13	0.025	0.0213	-0.0233	0.0727	-0.047	0.035	0.0104	0.0036	0.0173	0.0407	-0.0207	0.0012	-0.0236	0.0053	0.01	0.0197	-0.0117	-0.0124	0.0391	0.0128	0.0415	12.2488	73.132	100.8399
14	0.0272	-0.015	0.0036	0.0495	-0.0341	0.0296	-0.0044	0.0062	0.0243	-0.0436	-0.0149	-0.0202	0.0275	0.0057	-0.0239	0.0704	0.0374	-0.0247	0.026	0.0015	0.0538	18.5567	32.6486	95.1987
15	0.0021	-0.0003	-0.0027	0.0007	0.001	0.003	0.0032	0.0037	-0.0094	0.0041	0.007	0.014	0.0145	-0.0029	0.006	0.1181	-0.0109	-0.0229	0.042	-0.0078	0.1015	7.2725	25.9209	95.1344
16	0.141	0.055	0.0474	0.1358	-0.0089	0.0226	0.0308	-0.0156	-0.0106	-0.0785	-0.0112	0.0558	0.0491	-0.0096	0.0045	0.0554	0.0187	0.0012	0.0295	0.0137	0.0279	12.5545	40.3662	90.3152

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 117 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 26 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 27 through 38 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 39 through 54 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 55 through 64 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 117 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 26 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 27 through 54 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 55 through 64 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 117 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 53 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 54 through 64 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 65 through 117 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi