PDB-3can: Crystal structure of a domain of pyruvate-formate lyase-activatin...

ID or keywords:

Entry

Database: PDB / ID: 3can

Title

Crystal structure of a domain of pyruvate-formate lyase-activating enzyme from Bacteroides vulgatus ATCC 8482

Components

Pyruvate-formate lyase-activating enzyme

Keywords

LYASE ACTIVATOR / structural genomics / pyruvate-formate lyase-activating enzyme / PSI / MCSG / APC20359.1 / Protein Structure Initiative / Midwest Center for Structural Genomics / Iron / Iron-sulfur / Metal-binding

Function / homology

Function and homology information

[formate-C-acetyltransferase]-activating enzyme / [formate-C-acetyltransferase]-activating enzyme activity / 4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Bacteroides vulgatus ATCC 8482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Nocek, B. / Hendricks, R. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of a domain of pyruvate-formate lyase-activating enzyme from Bacteroides vulgatus ATCC 8482.
Authors: Nocek, B. / Hendricks, R. / Hatzos, C. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Feb 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3can.cif.gz	47.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3can.ent.gz	38.3 KB	Display	PDB format
PDBx/mmJSON format	3can.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3can_validation.pdf.gz	422.8 KB	Display	wwPDB validaton report
Full document	3can_full_validation.pdf.gz	424.1 KB	Display
Data in XML	3can_validation.xml.gz	10.1 KB	Display
Data in CIF	3can_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ca/3can ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3can	HTTPS FTP

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Related structure data

Similar structure data	6c8v-d 6ud0-d 6tjh-2 5l37-d 5ckt-2 6whh-d 5j3w-1 6tjc-d 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	TargetDB: APC20359.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (4) #111 - Mar 2009 Hydrogenase similarity (4) #144 - Dec 2011 Complex I similarity (4) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (4) #22 - Oct 2001 Photosystem I similarity (4) #66 - Jun 2005 Carotenoid Oxygenase similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (4)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#220 - Apr 2018
Dehalogenases
similarity (4)
#111 - Mar 2009
Hydrogenase
similarity (4)
#144 - Dec 2011
Complex I
similarity (4)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (4)
#154 - Oct 2012
Citric Acid Cycle
similarity (4)
#22 - Oct 2001
Photosystem I
similarity (4)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (4)
#241 - Jan 2020
Twenty Years of Molecules
similarity (4)

Deposited unit

A: Pyruvate-formate lyase-activating enzyme

20.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyruvate-formate lyase-activating enzyme

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

Unit cell

Length a, b, c (Å)	73.768, 73.768, 101.358
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-316- HOH

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

#1: Protein	Pyruvate-formate lyase-activating enzyme Mass: 20436.084 Da / Num. of mol.: 1 / Fragment: Domain: Residues 124-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria) Species: Bacteroides vulgatus / Strain: DSM 1447 / NCTC 11154 / Gene: BVU_1420 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6L094
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Pyruvate-formate lyase-activating enzyme

Mass: 20436.084 Da / Num. of mol.: 1 / Fragment: Domain: Residues 124-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacteroides vulgatus ATCC 8482 (bacteria)
Species: Bacteroides vulgatus / Strain: DSM 1447 / NCTC 11154 / Gene: BVU_1420 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6L094

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.37 Å³/Da / Density % sol: 63.54 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 60% v/v Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 / Details: Mirrors
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.8→35 Å / Num. all: 26922 / Num. obs: 26654 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / R_merge(I) obs: 0.076 / Net I/σ(I): 47
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 14.5 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELX		phasing
Coot		model building
MLPHARE		phasing
PHENIX		phasing
REFMAC		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.8→35 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.87 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	1343	5.1 %	RANDOM
R_work	0.162	-	-	-
all	0.168	26654	-	-
obs	0.163	26580	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.573 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.29 Å²	0 Å²	0 Å²
2-	-	0.29 Å²	0 Å²
3-	-	-	-0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1267	0	0	174	1441

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1329
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	915
X-RAY DIFFRACTION	r_angle_refined_deg	1.144	1.99	1807
X-RAY DIFFRACTION	r_angle_other_deg	0.842	3	2256
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.088	5	171
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.39	24.754	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.153	15	248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.011	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	211
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1465
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	244
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	259
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	1003
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	655
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	697
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	102
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.19	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.28	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.255	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	0.851	1.5	1033
X-RAY DIFFRACTION	r_mcbond_other	0.151	1.5	330
X-RAY DIFFRACTION	r_mcangle_it	1.079	2	1344
X-RAY DIFFRACTION	r_scbond_it	1.821	3	546
X-RAY DIFFRACTION	r_scangle_it	2.714	4.5	458

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.194	84	-
R_work	0.177	1835	-
all	-	1919	-
obs	-	-	99.64 %

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	0.7156	-0.1581	-2.8145	1.0011	-1.4966	15.7136	0.0303	0.0656	0.0686	0.0597	0.1086	0.0601	-0.0749	-0.2963	-0.1389	0.066	-0.009	0.0109	0.0647	0.0039	0.078	14.3115	-11.971	28.1087
2	0.3827	0.088	-0.2467	0.625	-0.3727	2.4381	0.0099	0.0881	-0.0706	0.1204	-0.02	-0.1753	-0.1003	-0.0078	0.0101	0.0798	0.0189	-0.0089	0.0645	-0.0061	0.0826	22.8086	-15.9581	27.5402
3	0.9181	-0.6371	-0.6006	2.7436	0.7241	0.7268	-0.0678	-0.0665	-0.0432	0.3	0.0442	-0.2711	-0.0033	0.0389	0.0236	0.1058	-0.0024	-0.0396	0.0548	0	0.0872	24.0151	-7.1391	34.6285
4	2.6312	-2.2203	-2.9126	2.9185	3.3352	3.9609	0.0357	-0.001	-0.096	0.0736	-0.0961	-0.0035	-0.0754	0.0122	0.0604	0.119	0.0064	0.0178	0.0398	0.0037	0.0539	17.0684	-1.4361	32.5794
5	2.734	-1.1209	-2.5718	10.4517	1.2615	15.3851	-0.1136	-0.3075	-0.01	0.3146	-0.0712	-0.0066	1.1113	0.2344	0.1848	0.1933	-0.0452	0.0428	0.0284	-0.0508	0.0136	8.8828	0.9808	47.6644
6	38.7324	13.6894	-42.8491	19.8678	1.4279	65.6768	-0.2671	2.5984	-0.0446	-0.9755	-0.2514	0.2905	2.9454	-2.8818	0.5185	0.4094	-0.0476	-0.0234	-0.0412	0.0428	-0.0838	8.025	-3.02	46.2962
7	21.4084	6.2392	-8.8547	7.4187	-10.2079	24.8455	-0.3539	-0.5684	-0.2115	-0.0553	-0.3568	-0.3964	0.8589	0.4348	0.7107	0.135	0.0184	0.0312	-0.0064	-0.0208	0.0115	18.2551	1.9679	42.8633
8	5.656	-1.9296	-1.4603	4.457	4.0408	3.6808	-0.1631	-0.1848	0.0444	0.1541	0.1869	-0.2806	0.0614	0.3617	-0.0238	0.0859	-0.0193	0.0073	0.0234	-0.0142	0.0869	24.6346	3.0224	32.3421
9	6.9868	-1.1565	-4.3949	1.9413	1.9627	3.6364	-0.0851	0.0304	-0.47	-0.0767	-0.3667	0.1903	0.0351	-0.2124	0.4518	0.0741	-0.0067	-0.0123	0.0914	-0.0616	0.064	7.1682	3.0845	33.2733
10	3.3462	0.7768	-0.8416	2.2913	1.1737	1.2388	-0.0339	-0.024	0.125	-0.0202	-0.1391	0.1135	-0.132	-0.0588	0.173	0.108	-0.0005	-0.0078	0.0485	-0.039	0.067	9.2539	12.4626	37.7472
11	5.1199	1.431	-0.7286	1.8192	1.3089	1.7382	-0.0158	0.0459	0.0314	-0.3249	-0.0588	-0.0081	-0.2735	-0.0475	0.0746	0.1098	-0.001	-0.0059	0.0233	-0.0012	0.0497	15.4646	7.0776	28.2735
12	25.8787	1.5806	-3.6264	29.4821	20.0991	36.5114	0.0797	-1.1916	-0.6881	2.0821	-1.8302	1.9365	2.4682	-2.005	1.7505	0.1159	-0.2405	0.1836	0.2907	-0.3121	0.2165	-4.4797	-0.6341	35.4571
13	7.2358	5.2403	-4.4754	33.3417	-15.2097	12.3565	-0.0084	0.0557	0.1018	-0.1002	-0.5279	1.0961	0.1539	-1.075	0.5363	-0.187	-0.02	-0.0134	0.1935	-0.2937	0.1398	-5.9332	5.521	34.0173
14	32.8461	16.8441	-0.5852	9.3603	-2.8791	9.218	-0.1212	0.3709	1.0345	0.0227	-0.1719	0.6611	-0.5517	-0.7249	0.2931	0.0444	0.1268	-0.1132	0.1034	-0.1805	0.1442	-1.6894	12.7138	29.9779
15	4.5668	3.1882	1.6232	7.1278	2.2255	3.468	-0.0135	0.2144	0.139	-0.5635	-0.2179	0.1532	-0.4539	-0.2588	0.2315	0.1341	0.0517	-0.0778	0.0463	-0.0181	0.0156	8.2809	12.7385	27.4634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	7 - 16	4 - 13
2	X-RAY DIFFRACTION	2	A	A	17 - 37	14 - 34
3	X-RAY DIFFRACTION	3	A	A	38 - 55	35 - 52
4	X-RAY DIFFRACTION	4	A	A	56 - 69	53 - 66
5	X-RAY DIFFRACTION	5	A	A	70 - 74	67 - 71
6	X-RAY DIFFRACTION	6	A	A	75 - 80	72 - 77
7	X-RAY DIFFRACTION	7	A	A	81 - 86	78 - 83
8	X-RAY DIFFRACTION	8	A	A	87 - 97	84 - 94
9	X-RAY DIFFRACTION	9	A	A	98 - 108	95 - 105
10	X-RAY DIFFRACTION	10	A	A	109 - 123	106 - 120
11	X-RAY DIFFRACTION	11	A	A	124 - 135	121 - 132
12	X-RAY DIFFRACTION	12	A	A	136 - 158	133 - 155
13	X-RAY DIFFRACTION	13	A	A	159 - 164	156 - 161
14	X-RAY DIFFRACTION	14	A	A	165 - 170	162 - 167
15	X-RAY DIFFRACTION	15	A	A	171 - 185	168 - 182

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