PDB-9b9n: Crystal structure of FlcD from Pseudomonas aeruginosa bound to ir...

ID or keywords:

Entry

Database: PDB / ID: 9b9n

Title

Crystal structure of FlcD from Pseudomonas aeruginosa bound to iron (II) and substrate

Components

Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C

Keywords

OXIDOREDUCTASE / mono-iron dioxygenase

Function / homology

Function and homology information

pyrroloquinoline-quinone synthase / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Walker, M.E. / Grove, T.L. / Li, B. / Redinbo, M.R.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM148685	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM137286	United States

Citation

Journal: Acs Cent.Sci. / Year: 2024
Title: Structural Basis for Methine Excision by a Heme Oxygenase-like Enzyme.
Authors: Simke, W.C. / Walker, M.E. / Calderone, L.A. / Putz, A.T. / Patteson, J.B. / Vitro, C.N. / Zizola, C.F. / Redinbo, M.R. / Pandelia, M.E. / Grove, T.L. / Li, B.

History

Deposition	Apr 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Sep 18, 2024	Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9b9n.cif.gz	282.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9b9n.ent.gz		Display	PDB format
PDBx/mmJSON format	9b9n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9b9n_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9b9n_full_validation.pdf.gz	1.6 MB	Display
Data in XML	9b9n_validation.xml.gz	26.8 KB	Display
Data in CIF	9b9n_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/9b9n ftp://data.pdbj.org/pub/pdb/validation_reports/b9/9b9n	HTTPS FTP

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Related structure data

Related structure data	8w1qC 9b9mC 9b9oC C: citing same article (ref.)
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

Deposited unit

A: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C

B: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C

hetero molecules

81 kDa, 2 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)	124.953, 55.865, 96.462
Angle α, β, γ (deg.)	90.00, 96.88, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C / Pyrroloquinoline-quinone synthase Mass: 40240.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: pqqC_2, CAZ10_19980, DT376_18990, NCTC13621_03444, PAERUG_P19_London_7_VIM_2_05_10_05324 Production host: Escherichia coli (E. coli) References: UniProt: A0A0C7AN42, pyrroloquinoline-quinone synthase
#2: Chemical	ChemComp-A1AL2 / (2R)-2-{[(2Z)-2-(hydroxyimino)ethyl]sulfanyl}butanedioic acid Mass: 207.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₉NO₅S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.08 Å³/Da / Density % sol: 40.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M Tris HCl pH 8.5, 25 % (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 2.28→28.63 Å / Num. obs: 30091 / % possible obs: 99.3 % / Redundancy: 2 % / B_iso Wilson estimate: 46.93 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.04726 / R_pim(I) all: 0.04726 / R_rim(I) all: 0.06684 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.28→2.365 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.4915 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 2896 / CC_1/2: 0.591 / CC star: 0.862 / R_pim(I) all: 0.4915 / R_rim(I) all: 0.695 / % possible all: 96.24

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.28→28.63 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2525	2000	6.65 %
R_work	0.2047	-	-
obs	0.208	30083	99.37 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.28→28.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5188	0	2	128	5318

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	5346
X-RAY DIFFRACTION	f_angle_d	1.596	7267
X-RAY DIFFRACTION	f_dihedral_angle_d	18.223	754
X-RAY DIFFRACTION	f_chiral_restr	0.102	796
X-RAY DIFFRACTION	f_plane_restr	0.011	964

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 (%)
2.28-2.34	0.385	134	0.3158	1885	X-RAY DIFFRACTION	95
2.34-2.4	0.3099	142	0.2899	1987	X-RAY DIFFRACTION	100
2.4-2.47	0.3775	143	0.2698	2006	X-RAY DIFFRACTION	100
2.47-2.55	0.3249	143	0.2654	2008	X-RAY DIFFRACTION	100
2.55-2.65	0.2938	143	0.2568	2011	X-RAY DIFFRACTION	100
2.65-2.75	0.2927	142	0.2492	2004	X-RAY DIFFRACTION	100
2.75-2.88	0.3339	142	0.2493	1986	X-RAY DIFFRACTION	100
2.88-3.03	0.2874	143	0.243	2010	X-RAY DIFFRACTION	100
3.03-3.22	0.296	142	0.231	2000	X-RAY DIFFRACTION	100
3.22-3.47	0.2836	144	0.2197	2027	X-RAY DIFFRACTION	100
3.47-3.81	0.2263	143	0.1906	2009	X-RAY DIFFRACTION	99
3.81-4.36	0.2063	144	0.1688	2021	X-RAY DIFFRACTION	100
4.36-5.49	0.2281	146	0.168	2035	X-RAY DIFFRACTION	100
5.49-28.63	0.2023	149	0.1697	2094	X-RAY DIFFRACTION	99

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	6.8245	2.9956	-0.4975	7.7417	1.1152	6.7362	0.3386	-1.4397	-1.005	0.6296	-0.4811	-0.3774	0.7283	0.0083	0.0606	0.5899	0.0215	0.0002	0.6115	0.244	0.5058	40.1964	-16.6239	33.1656
2	6.9475	-0.7717	1.6061	4.9812	-0.6903	3.5046	-0.093	-0.3893	-0.8816	-0.0507	-0.0578	0.2402	0.4854	-0.4133	0.1589	0.4037	-0.0266	0.071	0.3735	0.0432	0.3584	34.1052	-12.8197	23.5285
3	2.0479	0.0147	-1.0973	3.2372	-2.6527	5.445	0.0083	1.2211	0.771	-0.3974	0.0354	0.959	-0.5013	-1.1624	-0.1009	0.5073	0.0786	-0.1287	1.1211	0.2126	0.9617	18.5228	9.6247	12.4828
4	6.8607	0.7458	1.9944	7.7834	0.4231	1.9478	-0.0879	-0.237	0.7529	-0.0424	-0.5729	1.1314	-0.1969	-0.2023	0.3686	0.9319	0.331	0.0609	1.0508	-0.1905	0.6864	12.2204	9.1706	37.1012
5	4.9431	-0.1892	-1.874	2.1121	0.2191	2.6638	0.0905	-0.9687	0.7501	0.5771	0.0255	0.1934	-0.4419	-0.1021	-0.0666	0.5195	0.0896	0.0021	0.5408	-0.1654	0.3806	30.3724	7.9976	33.2593
6	2.975	0.8441	-0.9609	2.5429	0.1998	7.3163	0.1316	-0.3265	1.421	0.6038	-0.2325	0.2319	-0.823	-0.8346	-0.1204	0.6931	0.159	0.0874	0.613	-0.1884	0.8247	28.3391	17.8346	28.549
7	7.3316	1.2123	-4.5864	2.7063	-1.49	9.3193	-0.4387	0.2695	0.0403	0.2479	0.0802	0.2366	0.1844	-1.2647	0.3828	0.3353	0.069	0.014	0.4832	-0.0863	0.3854	19.4076	1.6653	25.9643
8	8.501	-0.0335	-0.9223	4.5072	0.3208	5.9183	-0.3059	0.3163	-0.5749	-0.2586	-0.0664	-0.3501	0.5657	0.0249	0.329	0.3766	-0.0085	0.0753	0.2513	0.0044	0.307	54.2303	-6.2474	9.8345
9	0.2305	-0.084	1.2447	0.7297	-0.8225	7.172	0.0609	-1.9102	0.0781	0.6944	-0.417	-1.1781	-0.2189	1.3768	0.3986	0.6925	-0.1824	-0.1605	1.6548	0.0328	0.8724	69.3331	2.3391	36.2698
10	2.1175	-1.3144	0.7161	1.8664	-0.2906	2.2653	-0.4343	-0.4066	0.9287	0.6537	-0.0682	-0.1753	-0.6216	1.0401	0.3928	0.6895	-0.257	-0.3548	0.8153	-0	1.6863	73.3992	21.2658	18.3068
11	5.1934	0.1366	-0.8945	2.4895	-0.0733	2.2491	0.0099	-0.0787	1.4461	0.0929	-0.0633	-0.0879	-0.4426	0.2473	0.0391	0.4023	-0.0342	-0.132	0.2891	0.0163	0.6789	54.4017	13.7062	18.2804
12	2.3686	3.3358	-2.1114	8.971	-4.4178	3.2924	0.7678	-1.1242	1.575	0.9685	-1.2818	-0.4929	-1.1651	0.839	0.486	0.7406	-0.1403	-0.1794	0.7725	-0.1686	1.2154	62.8332	18.4253	25.6308
13	2.1029	1.7408	-2.18	2.1616	-3.6626	6.9226	0.068	-0.9053	1.4333	0.9163	-0.1326	-0.2	-1.4552	0.3747	0.0321	0.9432	-0.0799	-0.1258	0.7071	-0.2268	1.1542	56.9092	19.1378	30.5574
14	6.3999	1.1872	-0.6474	6.8907	-3.6059	2.8784	-0.2826	-0.9106	0.3105	0.2313	-0.7994	-1.3144	-0.2396	1.3532	0.8926	0.3438	-0.0372	-0.1494	0.6268	0.0032	0.6682	68.4689	6.9999	21.4253

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 93 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 94 through 119 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 136 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 137 through 260 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 261 through 295 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 296 through 327 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 93 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 94 through 119 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 120 through 136 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 137 through 233 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 234 through 261 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 262 through 295 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 296 through 327 )

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