PDB-6ask: Crystal Structure of apo Flavin monooxygenase CmoJ (earlier YtnJ)

ID or keywords:

Entry

Database: PDB / ID: 6ask

Title

Crystal Structure of apo Flavin monooxygenase CmoJ (earlier YtnJ)

Components

Putative monooxygenase MoxC

Keywords

FLAVOPROTEIN / OXIDOREDUCTASE / Flavin monooxygenase

Function / homology

Function and homology information

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Bhandari, D.M. / Zhao, B. / Li, P. / Begley, T.P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Flavin mediated Pummerer type rearrangement in cysteine salvage pathway
Authors: Bhandari, D.M. / Krishnamoorthy, K. / Zhao, B. / Li, P. / Begley, T.P.

History

Deposition	Aug 24, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	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

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Download

PDBx/mmCIF format	6ask.cif.gz	188.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ask.ent.gz	149.8 KB	Display	PDB format
PDBx/mmJSON format	6ask.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ask_validation.pdf.gz	424.3 KB	Display	wwPDB validaton report
Full document	6ask_full_validation.pdf.gz	429.5 KB	Display
Data in XML	6ask_validation.xml.gz	19.3 KB	Display
Data in CIF	6ask_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/6ask ftp://data.pdbj.org/pub/pdb/validation_reports/as/6ask	HTTPS FTP

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Related structure data

Related structure data	6aslC 1yw1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6kcx-1 6asl-1 4wd3-d 2nqq-1 2v5a-d 7brf-1 7c9a-d 3u95-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (3)

Deposited unit

A: Putative monooxygenase MoxC

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

1

A: Putative monooxygenase MoxC

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

Unit cell

Length a, b, c (Å)	86.751, 86.751, 195.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-752- HOH

#1: Protein	Putative monooxygenase MoxC Mass: 49669.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: moxC, ytnJ, BSU29310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O34974, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative monooxygenase MoxC

Mass: 49669.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: moxC, ytnJ, BSU29310 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O34974, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.7 Å³/Da / Density % sol: 66.77 % / Description: diamond shaped
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM HEPES pH7.5, 200 mM KCl, 29%-33% pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.69→64.87 Å / Num. obs: 84371 / % possible obs: 100 % / Redundancy: 21.2 % / R_merge(I) obs: 0.14 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.69→1.74 Å / Redundancy: 23.4 % / R_merge(I) obs: 1.884 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
iMOSFLM	7.2.1	data processing
iMOSFLM	7.2.1	data scaling
PHENIX	(1.10.1_2155: ???)	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YW1

1yw1

Resolution: 1.69→64.87 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.71

	R_factor	Num. reflection	% reflection
R_free	0.19	4222	5.01 %
R_work	0.174	-	-
obs	0.175	84230	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.69→64.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3400	0	0	296	3696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3506
X-RAY DIFFRACTION	f_angle_d	0.75	4751
X-RAY DIFFRACTION	f_dihedral_angle_d	19.43	2082
X-RAY DIFFRACTION	f_chiral_restr	0.054	507
X-RAY DIFFRACTION	f_plane_restr	0.006	632

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 (%)
1.689-1.7082	0.2789	132	0.2751	2652	X-RAY DIFFRACTION	100
1.7082-1.7283	0.3021	135	0.2686	2606	X-RAY DIFFRACTION	100
1.7283-1.7494	0.3058	154	0.2593	2622	X-RAY DIFFRACTION	100
1.7494-1.7715	0.2567	153	0.2293	2614	X-RAY DIFFRACTION	100
1.7715-1.7949	0.2399	140	0.2209	2605	X-RAY DIFFRACTION	100
1.7949-1.8194	0.2389	121	0.212	2653	X-RAY DIFFRACTION	100
1.8194-1.8454	0.2049	145	0.1947	2658	X-RAY DIFFRACTION	100
1.8454-1.873	0.2134	126	0.1882	2604	X-RAY DIFFRACTION	100
1.873-1.9023	0.254	136	0.2347	2643	X-RAY DIFFRACTION	100
1.9023-1.9334	0.3968	136	0.3789	2607	X-RAY DIFFRACTION	98
1.9334-1.9668	0.2432	139	0.2111	2626	X-RAY DIFFRACTION	100
1.9668-2.0026	0.1846	128	0.1772	2650	X-RAY DIFFRACTION	100
2.0026-2.0411	0.2016	140	0.1763	2651	X-RAY DIFFRACTION	100
2.0411-2.0827	0.2352	126	0.2388	2626	X-RAY DIFFRACTION	100
2.0827-2.128	0.1803	152	0.1693	2652	X-RAY DIFFRACTION	100
2.128-2.1775	0.1655	150	0.161	2641	X-RAY DIFFRACTION	100
2.1775-2.232	0.198	133	0.1703	2654	X-RAY DIFFRACTION	100
2.232-2.2923	0.239	150	0.2378	2611	X-RAY DIFFRACTION	99
2.2923-2.3598	0.1819	154	0.1655	2653	X-RAY DIFFRACTION	100
2.3598-2.436	0.2049	157	0.1681	2625	X-RAY DIFFRACTION	100
2.436-2.523	0.1924	134	0.1647	2684	X-RAY DIFFRACTION	100
2.523-2.6241	0.1788	138	0.1676	2687	X-RAY DIFFRACTION	100
2.6241-2.7435	0.1943	151	0.1639	2658	X-RAY DIFFRACTION	100
2.7435-2.8881	0.1624	127	0.1594	2713	X-RAY DIFFRACTION	100
2.8881-3.0691	0.1844	119	0.1554	2717	X-RAY DIFFRACTION	100
3.0691-3.306	0.1418	127	0.1549	2726	X-RAY DIFFRACTION	100
3.306-3.6387	0.159	161	0.1491	2697	X-RAY DIFFRACTION	100
3.6387-4.1651	0.1643	139	0.1451	2743	X-RAY DIFFRACTION	100
4.1651-5.2473	0.149	149	0.1442	2790	X-RAY DIFFRACTION	100
5.2473-64.92	0.2093	170	0.1805	2940	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	0.5758	0.0503	-0.1078	0.5808	0.3382	1.3239	-0.0137	-0.0712	0.062	0.0106	0.0195	-0.0451	-0.1693	0.1088	-0.0052	0.1864	-0.0349	-0.0109	0.1684	0.0007	0.1979	20.7837	-6.1018	-40.2502
2	2.8383	0.1665	0.4921	3.3836	1.4154	3.9422	0.4667	-0.5215	-0.4746	0.5772	0.0546	-0.8012	0.9753	0.3803	-0.3441	0.8767	-0.0582	-0.2612	0.4452	0.0047	0.6235	19.3522	-11.9894	-3.9644
3	0.9432	0.1209	0.0779	1.4792	0.4071	3.3938	-0.044	0.0057	0.0644	-0.1917	0.0417	-0.0084	-0.5119	-0.0069	-0.0088	0.2923	-0.004	-0.0247	0.1448	-0.0376	0.2204	17.146	9.1466	-30.3936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 3 THROUGH 292 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 293 THROUGH 357 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 358 THROUGH 432 )

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