PDB-6fzi: Crystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroe...

ID or keywords:

Entry

Database: PDB / ID: 6fzi

Title

Crystal Structure of a Clostridial Dehydrogenase at 2.55 Angstroems Resolution

Components

Glyceraldehyde-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / Clostridium perfringens / GAPDH / NAD / dehydrogenase / anacardic acid / curcumin / complement / C5a / C3a / C3

Function / homology

Function and homology information

Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function

Biological species

Clostridium perfringens SM101 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Gomez, S. / Querol-Garcia, J. / Sanchez-Barron, G. / Subias, M. / Gonzalez-Alsina, A. / Melchor-Tafur, C. / Franco-Hidalgo, V. / Alberti, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.

Funding support

Spain,

Belgium, 7items

Organization	Grant number	Country
Instituto de Salud Carlos III	PI12/01667	Spain
Spanish Ministry of Economy and Competitiveness	CTQ2015-66206-C2-2-R	Spain
Spanish Ministry of Economy and Competitiveness	SAF2015-72961-EXP	Spain
Spanish Network of Excellence on Complement	SAF2016-81876-REDT	Spain
Regional Government of Madrid	S2010/BD-2316	Spain
Regional Government of Madrid	S2017/BMD-3673	Spain
European Commission, FP7 Programme	ComplexINC (Contract No. 279039)	Belgium

Citation

Journal: Front Microbiol / Year: 2019
Title: The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human ...
Authors: Gomez, S. / Querol-Garcia, J. / Sanchez-Barron, G. / Subias, M. / Gonzalez-Alsina, A. / Franco-Hidalgo, V. / Alberti, S. / Rodriguez de Cordoba, S. / Fernandez, F.J. / Vega, M.C.

History

Deposition	Mar 14, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6fzi.cif.gz	514.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6fzi.ent.gz	428.6 KB	Display	PDB format
PDBx/mmJSON format	6fzi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6fzi_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6fzi_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6fzi_validation.xml.gz	50.8 KB	Display
Data in CIF	6fzi_validation.cif.gz	67.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fz/6fzi ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fzi	HTTPS FTP

-
Related structure data

Related structure data	6fzhSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3pym-1 3lc7-d 6fzh-1 3ksd-d 1dc5-2 7jwk-d 5jye-d 3doc-d 3k9q-d 4lsm-2 Search similar-shape structures by Omokage search (details) 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	#50 - Feb 2004 Glycolytic Enzymes similarity (9)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.280, 101.610, 92.820
Angle α, β, γ (deg.)	90.00, 107.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 35400.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens SM101 (bacteria) Gene: gap, CPR_1301 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta pLysS References: UniProt: Q0STD4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase

Mass: 35400.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium perfringens SM101 (bacteria)
Gene: gap, CPR_1301 / Plasmid: pETM-11 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta pLysS
References: UniProt: Q0STD4, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 5 types, 87 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M sodium acetate, 20% w/v PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2014 / Details: KIRKPATRICK-BAEZ FOCUSING SYSTEM
Radiation	Monochromator: CHANNEL-CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.55→57.67 Å / Num. obs: 42341 / % possible obs: 99.61 % / Redundancy: 4.2 % / B_iso Wilson estimate: 67.2 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.07224 / R_pim(I) all: 0.0391 / R_rim(I) all: 0.08253 / Net I/σ(I): 12.66
Reflection shell	Resolution: 2.55→2.641 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.9875 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 4184 / CC_1/2: 0.605 / R_pim(I) all: 0.5292 / R_rim(I) all: 1.126 / % possible all: 99.71

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS	January 10, 2014	data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6FZH

6fzh

Resolution: 2.55→54.783 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 25.62

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.215	4093	4.99 %	RANDOM SELECTION
R_work	0.1636	-	-	-
obs	0.1662	42320	98.36 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 72.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→54.783 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9914	0	292	61	10267

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10365
X-RAY DIFFRACTION	f_angle_d	1.167	14060
X-RAY DIFFRACTION	f_dihedral_angle_d	16.723	6211
X-RAY DIFFRACTION	f_chiral_restr	0.065	1657
X-RAY DIFFRACTION	f_plane_restr	0.007	1803

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 (%)
2.55-2.58	0.4212	139	0.3319	2588	X-RAY DIFFRACTION	97
2.58-2.6115	0.3776	141	0.3144	2730	X-RAY DIFFRACTION	98
2.6115-2.6445	0.3535	142	0.2911	2680	X-RAY DIFFRACTION	99
2.6445-2.6793	0.3185	143	0.2794	2691	X-RAY DIFFRACTION	98
2.6793-2.716	0.3335	142	0.265	2704	X-RAY DIFFRACTION	99
2.716-2.7548	0.3368	139	0.2596	2637	X-RAY DIFFRACTION	98
2.7548-2.7959	0.3159	143	0.2605	2758	X-RAY DIFFRACTION	99
2.7959-2.8396	0.3358	137	0.2659	2623	X-RAY DIFFRACTION	98
2.8396-2.8862	0.3052	141	0.2643	2667	X-RAY DIFFRACTION	99
2.8862-2.9359	0.2927	140	0.2343	2734	X-RAY DIFFRACTION	98
2.9359-2.9893	0.2668	140	0.2276	2712	X-RAY DIFFRACTION	99
2.9893-3.0468	0.3267	144	0.2277	2693	X-RAY DIFFRACTION	99
3.0468-3.109	0.2739	145	0.209	2682	X-RAY DIFFRACTION	99
3.109-3.1766	0.2584	143	0.2068	2727	X-RAY DIFFRACTION	99
3.1766-3.2505	0.2773	138	0.1985	2614	X-RAY DIFFRACTION	97
3.2505-3.3318	0.2399	143	0.1908	2694	X-RAY DIFFRACTION	97
3.3318-3.4218	0.2268	135	0.1755	2672	X-RAY DIFFRACTION	98
3.4218-3.5225	0.1958	144	0.1702	2702	X-RAY DIFFRACTION	98
3.5225-3.6362	0.2373	145	0.1617	2672	X-RAY DIFFRACTION	98
3.6362-3.7661	0.2242	142	0.158	2649	X-RAY DIFFRACTION	98
3.7661-3.9169	0.2093	145	0.1447	2766	X-RAY DIFFRACTION	99
3.9169-4.0951	0.1907	142	0.1336	2674	X-RAY DIFFRACTION	99
4.0951-4.3109	0.1831	145	0.1287	2733	X-RAY DIFFRACTION	98
4.3109-4.5809	0.1716	140	0.1133	2678	X-RAY DIFFRACTION	98
4.5809-4.9343	0.1587	138	0.1221	2683	X-RAY DIFFRACTION	99
4.9343-5.4305	0.1765	140	0.1186	2711	X-RAY DIFFRACTION	99
5.4305-6.2154	0.2165	140	0.1397	2709	X-RAY DIFFRACTION	98
6.2154-7.8271	0.1676	138	0.1546	2679	X-RAY DIFFRACTION	98
7.8271-54.7959	0.1618	139	0.1346	2674	X-RAY DIFFRACTION	98

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	2.8932	0.0197	0.432	2.7351	0.504	6.0968	0.0497	0.1596	-0.2234	-0.1221	-0.0115	0.79	0.6401	-0.9711	-0.0488	0.5206	-0.0833	-0.0763	0.5556	0.0603	0.7141	-16.7789	-13.5593	16.6243
2	1.8972	-0.0583	-0.2589	1.6641	-0.2244	2.2083	0.0498	0.5382	0.2228	-0.625	0.0544	0.4075	-0.0807	-0.4081	-0.1035	0.5347	0.0202	-0.1057	0.5345	0.063	0.477	-3.1138	1.7785	1.2385
3	3.232	0.2802	-1.1787	7.5008	-1.7003	5.3277	-0.1585	0.2477	-0.568	-0.4391	0.0305	-0.6298	1.1604	0.7147	0.1396	0.6229	0.1506	0.0012	0.5659	-0.0833	0.478	22.6453	-25.3571	22.0302
4	1.9676	0.1782	0.843	1.9389	-0.1929	3.3368	0.135	-0.2581	-0.1138	0.354	-0.0578	-0.1809	0.2602	0.4266	-0.0664	0.3942	0.0162	0.0041	0.4774	-0.0009	0.3814	17.684	-9.5352	42.2195
5	5.7786	2.3486	-0.1029	5.8667	-1.8938	6.9655	-0.0089	-0.1188	0.3714	-0.3086	-0.187	-0.7825	-0.4444	1.7098	0.204	0.5121	-0.1012	0.0479	0.8095	0.0186	0.5262	34.11	12.121	23.093
6	2.2375	0.0147	0.1954	2.396	-0.1232	6.0453	-0.1931	0.0113	0.9774	0.6295	-0.3399	-0.3782	-2.2989	1.4848	0.4834	1.0886	-0.3294	-0.0669	0.9074	0.0918	0.8143	35.8725	23.7253	17.5219
7	5.8131	4.6739	-1.2333	8.0912	-1.2553	2.5509	-0.3796	0.0935	-0.19	-0.6524	-0.3592	-1.4361	-0.6268	1.2415	0.6627	0.6724	-0.11	0.0153	1.0188	0.2355	0.6672	35.9253	16.5758	0.4311
8	2.2609	-0.0706	-1.4205	1.337	-0.4823	4.3306	0.0712	0.3848	0.199	-0.454	-0.0367	-0.0557	-0.4489	0.176	-0.0722	0.5428	-0.0353	0.012	0.5279	0.0929	0.5175	16.3766	9.255	1.7024
9	2.0598	0.1851	0.5288	3.0397	0.3278	3.4124	-0.0781	0.4627	0.0847	-0.3943	-0.0298	-0.3362	0.0912	0.6837	0.0953	0.4539	0.0267	0.0939	0.6001	0.0522	0.4189	24.3535	1.7511	2.271
10	1.9275	-0.0661	0.1544	4.5683	0.6124	6.8135	0.2364	0.0755	0.7085	0.1014	0.0744	0.951	-0.8953	-0.8171	-0.209	0.6143	0.1202	0.1061	0.4661	0.1037	0.8384	-7.2014	23.9262	25.3682
11	1.7272	0.214	0.5378	2.6473	-0.2399	5.9396	0.0343	-0.0687	0.7639	0.2411	0.0975	0.4053	-1.5804	-0.2133	-0.1511	0.8185	0.0769	0.1933	0.5092	-0.0293	0.8915	-3.6073	30.916	36.5383
12	2.685	-0.1679	-1.12	1.1806	0.3768	3.5953	0.1078	-0.3213	0.3783	0.3449	-0.0434	0.2676	-0.3833	-0.0216	-0.0846	0.4694	0.003	0.0604	0.3597	-0.0451	0.4958	2.2541	6.6015	43.4043
13	3.2656	-0.1856	-0.2775	2.3011	-0.1995	4.3454	0.0131	-0.1636	0.3484	0.1534	-0.0923	-0.0601	-0.2612	-0.2486	0.0596	0.4292	-0.0254	0.1467	0.3783	-0.01	0.5004	-3.751	8.4127	45.3078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 128 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 129 through 331 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 118 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 119 through 332 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 2 through 56 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 57 through 128 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 129 through 149 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 150 through 264 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 265 through 332 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 56 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 57 through 149 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 150 through 294 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 295 through 332 )

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 87 molecules

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 87 molecules

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 87 molecules

-
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