PDB-7tg5: Crystal Structure of the Pirin Family Protein Redox-sensitive Bic...

ID or keywords:

Entry

Database: PDB / ID: 7tg5

Title

Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK in the Presence of Fe Ion from Yersinia pestis

Components

Pirin family protein

Keywords

METAL BINDING PROTEIN / Pirin Family Protein / Bicupin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Yersinia pestis CO92 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.72 Å

Authors

Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK in the presence of Fe ion from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 7, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2022	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7tg5.cif.gz	280.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7tg5.ent.gz	196 KB	Display	PDB format
PDBx/mmJSON format	7tg5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7tg5_validation.pdf.gz	819.6 KB	Display	wwPDB validaton report
Full document	7tg5_full_validation.pdf.gz	822.6 KB	Display
Data in XML	7tg5_validation.xml.gz	24.1 KB	Display
Data in CIF	7tg5_validation.cif.gz	35 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tg/7tg5 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tg5	HTTPS FTP

-
Related structure data

Related structure data	7te5
Similar structure data	7te5-2 6bc4-d 6mn4-2 6mn4-5 6mn3-2 6mn4-4 5q0p-2 5q0p-1 6bc3-d 5q0j-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP64164

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pirin family protein

B: Pirin family protein

hetero molecules

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

1

A: Pirin family protein

hetero molecules

defined by author&software
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pirin family protein

hetero molecules

defined by author&software
32.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.050, 66.050, 121.540
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁
Space group name Hall	P3₁
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3

#1: Protein	Pirin family protein / Pirin-related protein / Yhak Mass: 32142.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: yp02149 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A2U2H063
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium acetate, 0.1 M MES pH 6.5, 30 %(w/v) PEG 2000 MME

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 1.72→50 Å / Num. obs: 62979 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.994 / R_merge(I) obs: 0.111 / Net I/σ(I): 24.1
Reflection shell	Resolution: 1.72→1.75 Å / R_merge(I) obs: 1.586 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 3179 / CC_1/2: 0.436 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.72→31.87 Å / Cross valid method: FREE R-VALUE / σ(F): 2.45 / Phase error: 22.2145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2077	3010	4.79 %
R_work	0.1714	59854	-
obs	0.1738	62864	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→31.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4364	0	3	327	4694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	4511
X-RAY DIFFRACTION	f_angle_d	0.6418	6141
X-RAY DIFFRACTION	f_chiral_restr	0.0474	655
X-RAY DIFFRACTION	f_plane_restr	0.004	821
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6897	1627

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 (%)
1.72-1.75	0.2983	141	0.2925	2993	X-RAY DIFFRACTION	94.54
1.75-1.78	0.312	212	0.2672	2933	X-RAY DIFFRACTION	92.79
1.78-1.82	0.2969	130	0.2615	3003	X-RAY DIFFRACTION	95.67
1.82-1.85	0.3053	164	0.2485	2984	X-RAY DIFFRACTION	94.52
1.85-1.89	0.1992	113	0.2315	3060	X-RAY DIFFRACTION	96.35
1.89-1.94	0.2636	165	0.2151	2960	X-RAY DIFFRACTION	94.57
1.94-1.99	0.2532	136	0.2145	2984	X-RAY DIFFRACTION	95.58
1.99-2.04	0.2524	114	0.2117	3029	X-RAY DIFFRACTION	96.37
2.04-2.1	0.2152	166	0.2119	2944	X-RAY DIFFRACTION	94.66
2.1-2.17	0.2646	154	0.2097	3027	X-RAY DIFFRACTION	95.13
2.17-2.25	0.1787	162	0.1977	2996	X-RAY DIFFRACTION	94.87
2.25-2.33	0.2749	128	0.2045	3008	X-RAY DIFFRACTION	95.92
2.34-2.44	0.2414	130	0.2012	3008	X-RAY DIFFRACTION	95.83
2.44-2.57	0.2142	154	0.1996	3005	X-RAY DIFFRACTION	95.13
2.57-2.73	0.2482	178	0.1894	2977	X-RAY DIFFRACTION	94.36
2.73-2.94	0.2216	156	0.1807	2994	X-RAY DIFFRACTION	95.02
2.94-3.24	0.2301	110	0.1625	3012	X-RAY DIFFRACTION	96.48
3.24-3.7	0.1732	130	0.1392	3031	X-RAY DIFFRACTION	95.86
3.71-4.66	0.153	157	0.1054	2983	X-RAY DIFFRACTION	95
4.67-31.87	0.1801	208	0.1349	2925	X-RAY DIFFRACTION	92.92

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	0.33320788107	0.172638198359	1.01150152965	0.738076763483	0.44298198357	3.84659570286	0.0298567651153	0.256905693385	-0.124896245156	-0.073678119945	-0.130278843624	0.0422397703271	-0.0218202019195	-0.480569070159	0.0973494046623	0.185354583362	0.00558426777221	-0.0326845421621	0.177727775297	-0.0104380760149	0.125823277406	-27.3111074225	52.3338345937	-3.03282312689
2	4.77121912396	-3.34565378623	-1.886190087	3.10436391961	0.61103776529	2.19779201933	0.214914805644	0.0519877728747	-0.320071999945	-0.151313125374	-0.255747234019	0.323885040816	-0.0562506759178	-0.443595270512	0.0724500432178	0.134545507457	-0.00962935062106	-0.0341771049672	0.237277202469	-0.0176253902072	0.162541959004	-25.1643252137	46.9018911949	1.62411987633
3	0.356829721544	-0.0166256682347	-0.475294773105	1.38880872895	0.718117876928	1.09587807171	0.0338340428957	-0.103024507245	-0.00326113712323	0.194511057525	-0.0209396646821	-0.0678757186525	0.0401673921377	0.0451201100742	-0.0312899956811	0.155458912842	0.0255587394869	-0.0205789514493	0.249970849495	0.00710111966185	0.127874168473	-22.8822562386	50.0133267117	17.6941390344
4	2.86169259902	-0.894092533054	-2.26707487208	1.49233260601	1.31319782631	5.61382706795	0.0360766669723	-0.0745551537589	-0.0399292451807	0.134448749108	-0.0203763417253	0.105532506219	-0.0511197015689	0.127267137929	0.000561722042791	0.133885317133	0.0034657384187	-0.0105791416227	0.190138581827	-0.00505255010975	0.10968665988	-25.7614711791	57.3252655543	18.1674887508
5	1.81156166097	0.931384962323	-0.166233806876	3.28316523829	-0.641944532862	1.62089418187	-0.036860723018	-0.133212079473	0.0364865751619	0.116198946204	0.0105834617606	-0.154789746745	-0.0800376938492	0.235151093178	0.0657234392679	0.103406422501	0.00860051966672	-0.0197935227125	0.246368772103	-0.0190257599393	0.120611061736	-9.43432389826	50.7739442581	6.72274404759
6	2.47333950955	-1.67240996114	0.833435948834	4.39425601892	-0.397948242581	0.834622947709	0.046138134421	0.143991533238	0.181221629818	-0.248058645458	-0.130898584201	-0.0423487694327	-0.0910849613795	0.0450838155986	0.0990336031198	0.184267604385	-0.00110346311798	-0.00827922664147	0.245724231359	0.00959812031164	0.0955796692027	-16.4669592476	58.1932805075	-7.71869413175
7	3.90572640534	2.63632771852	-2.69879834508	4.07004019268	-1.88864629248	2.94951932003	-0.324249363323	-0.123040056442	-0.487500723092	-0.0317433833083	0.0408167713712	-0.166914020835	0.495217521306	-0.0490010263188	0.305525067064	0.210069806818	0.00243986130088	-0.0193184942974	0.190737694894	0.0142048871058	0.149113184525	-22.5334314182	33.1841439362	7.67432933544
8	0.907936875182	-0.0893421171282	-1.36160525096	0.925935272204	0.558842561346	2.2032242366	0.148366263192	-0.146633200882	-0.0870307256588	0.0670003689397	0.00428408712787	0.00728459788661	-0.0234775730375	-0.186662273614	-0.0601608947019	0.172058898657	0.00107999995218	0.042853286035	0.220737513067	-0.0121219316617	0.116551319304	5.66234279119	43.1313895914	18.5795462739
9	0.810201691817	0.779853959176	0.818532048134	1.92941311042	0.9971030161	1.09084936699	0.0476060353259	0.076587940627	0.0145027249604	-0.0432243128834	-0.0444139134842	-0.0310315688467	0.0313534707217	0.0296041539341	0.000774957000795	0.139011922678	-0.00332324445515	0.0244319026514	0.237112554075	-0.00524928273308	0.111184902784	9.04856650039	44.6279100861	1.70978080816
10	2.05533087475	-1.03204256456	0.261495175644	3.72702257289	-0.837789106098	1.25695545226	-0.0765784084522	0.165046253578	-0.107319613473	-0.00104868203343	0.090662813395	-0.0245057934516	-0.0130222548119	0.195387095609	-0.0409549953811	0.114949724968	-0.0328004799702	0.0145476931608	0.259944271271	-0.023828416213	0.107661963486	23.6106073543	44.5782745904	8.46622700113
11	1.10003307471	-0.193395591209	0.380979332616	2.02459626307	-0.506428603344	0.841665262301	-0.00123289124668	-0.104122835437	0.0284485485877	0.126835842793	-0.0152081171331	0.0304654621351	0.0173583757504	0.0609799026757	0.0221552517307	0.131354692475	-0.00840818693312	0.0332213376976	0.234887265318	-0.0253977679178	0.0872939738544	14.3147276354	46.8594875323	17.200639569

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 0 through 19 )	A	A	0 - 19	1 - 20
2	2	chain 'A' and (resid 20 through 45 )	A	A	20 - 45	21 - 46
3	3	chain 'A' and (resid 46 through 105 )	A	A	46 - 105	47 - 106
4	4	chain 'A' and (resid 106 through 125 )	A	A	106 - 125	107 - 126
5	5	chain 'A' and (resid 126 through 185 )	A	A	126 - 185	127 - 186
6	6	chain 'A' and (resid 186 through 245 )	A	A	186 - 245	187 - 246
7	7	chain 'A' and (resid 246 through 283 )	A	A	246 - 283	247 - 284
8	8	chain 'B' and (resid 0 through 19 )	B	B	0 - 19	1 - 20
9	9	chain 'B' and (resid 20 through 125 )	B	B	20 - 125	21 - 126
10	10	chain 'B' and (resid 126 through 185 )	B	B	126 - 185	127 - 186
11	11	chain 'B' and (resid 186 through 283 )	B	B	186 - 283	187 - 284

-
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