PDB-3ihm: Structure of the oxygenase component of a Pseudomonas styrene mon...

ID or keywords:

Entry

Database: PDB / ID: 3ihm

Title

Structure of the oxygenase component of a Pseudomonas styrene monooxygenase

Components

Styrene monooxygenase A

Keywords

OXIDOREDUCTASE / Rossmann fold / anti-parallel beta strands / dimer / cavity

Function / homology

Function and homology information

styrene monooxygenase / monooxygenase activity
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS,

molecular replacement /

MIRAS /

molecular replacement / Resolution: 2.3 Å

Authors

Rosenzweig, A.C. / Ukaegbu, U.E. / Gassner, G.

Citation

Journal: Biochemistry / Year: 2010
Title: Structure and ligand binding properties of the epoxidase component of styrene monooxygenase
Authors: Ukaegbu, U.E. / Kantz, A. / Beaton, M. / Gassner, G.T. / Rosenzweig, A.C.

History

Deposition	Jul 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ihm.cif.gz	179.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3ihm.ent.gz	140.6 KB	Display	PDB format
PDBx/mmJSON format	3ihm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ihm_validation.pdf.gz	435.6 KB	Display	wwPDB validaton report
Full document	3ihm_full_validation.pdf.gz	442.6 KB	Display
Data in XML	3ihm_validation.xml.gz	34.8 KB	Display
Data in CIF	3ihm_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/3ihm ftp://data.pdbj.org/pub/pdb/validation_reports/ih/3ihm	HTTPS FTP

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Related structure data

Similar structure data	3b4w-1 3i44-1 4h73-4 3sq8-6 6pnu-3 6s6w-d 4v3f-2 3sq7-5 6jub-d 2ar9-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Styrene monooxygenase A

B: Styrene monooxygenase A

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

1

Idetical with deposited unit
defined by author

2

A: Styrene monooxygenase A

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

3

B: Styrene monooxygenase A

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

Unit cell

Length a, b, c (Å)	114.302, 114.302, 140.803
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Styrene monooxygenase A Mass: 48115.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S12 / Production host: Escherichia coli (E. coli) / References: UniProt: O33471*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.91 Å³/Da / Density % sol: 57.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 30% (w/v) PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-D	1	1.03
SYNCHROTRON	APS	21-ID-F	2	0.98

Detector

Type	ID	Detector	Date
MAR CCD 165 mm	1	CCD	Dec 1, 2008
MAR CCD 130 mm	2	CCD	Jun 4, 2009

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	graphite	SINGLE WAVELENGTH	M	x-ray	1
2	graphite	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.03	1
2	0.98	1

Reflection

Redundancy: 8 % / Av σ(I) over netI: 30.88 / Number: 168337 / R_merge(I) obs: 0.126 / Χ²: 1.94 / D res high: 3 Å / D res low: 50 Å / Num. obs: 21093 / % possible obs: 98.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.46	50	96.7	1	0.054	4.201	8
5.13	6.46	99.2	1	0.078	2.466	8.2
4.48	5.13	99.7	1	0.078	2.6	8.1
4.07	4.48	99.6	1	0.094	2.156	8.1
3.78	4.07	99.7	1	0.132	1.841	8.1
3.56	3.78	99.4	1	0.182	1.577	8.1
3.38	3.56	99.5	1	0.269	1.28	8.1
3.23	3.38	99.2	1	0.392	1.105	8
3.11	3.23	98.7	1	0.525	1.02	7.9
3	3.11	96.9	1	0.694	0.956	7.1

Reflection

Resolution: 2.27→50 Å / Num. obs: 48378 / % possible obs: 100 % / Redundancy: 11.6 % / R_merge(I) obs: 0.093 / Χ²: 1.204 / Net I/σ(I): 8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.27-2.31	11.6	0.378	2398	0.728	1,2	100
2.31-2.35	11.6	0.351	2402	0.732	1,2	100
2.35-2.4	11.6	0.312	2412	0.748	1,2	100
2.4-2.45	11.6	0.277	2421	0.734	1,2	100
2.45-2.5	11.6	0.251	2394	0.751	1,2	100
2.5-2.56	11.6	0.214	2419	0.721	1,2	100
2.56-2.62	11.6	0.196	2399	0.739	1,2	100
2.62-2.69	11.6	0.179	2410	0.733	1,2	100
2.69-2.77	11.6	0.159	2417	0.75	1,2	100
2.77-2.86	11.6	0.137	2437	0.784	1,2	100
2.86-2.96	11.6	0.122	2398	0.788	1,2	100
2.96-3.08	11.6	0.102	2424	0.827	1,2	100
3.08-3.22	11.6	0.086	2412	0.943	1,2	100
3.22-3.39	11.6	0.085	2401	1.294	1,2	100
3.39-3.6	11.6	0.084	2437	1.888	1,2	100
3.6-3.88	11.5	0.079	2417	2.26	1,2	100
3.88-4.27	11.4	0.076	2437	2.636	1,2	100
4.27-4.89	11.4	0.055	2417	2.203	1,2	100
4.89-6.16	11.6	0.042	2447	1.277	1,2	100
6.16-50	11.2	0.036	2479	2.591	1,2	99.9

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Phasing

Phasing

Method
MIRAS
molecular replacement

Phasing MR

R_factor: 34.2 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.27 Å	42.41 Å
Translation	2.27 Å	42.41 Å

Phasing MIR der

Resolution: 0→0.24 Å / Power acentric: 0.11 / Power centric: 3.02 / Reflection acentric: 18 / Reflection centric: 3

Phasing MIR der shell

Highest resolution: 0 Å / Lowest resolution: 0.24 Å / Power acentric: 0.42 / Power centric: 8.92 / Reflection acentric: 2 / Reflection centric: 12

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.1.2	phasing
SHARP		phasing
REFMAC	refmac_5.2.0019	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MIRAS,

molecular replacement / Resolution: 2.3→42.41 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.909 / WR_factor R_free: 0.233 / WR_factor R_work: 0.196 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.625 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	2340	5.1 %	RANDOM
R_work	0.206	-	-	-
obs	0.207	46247	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 76.37 Å² / B_iso mean: 18.854 Å² / B_iso min: 2.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0.03 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→42.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6429	0	0	578	7007

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	6585
X-RAY DIFFRACTION	r_angle_refined_deg	0.891	1.958	8931
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.847	5	813
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.535	23.62	326
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.283	15	1066
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.543	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	959
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	5128
X-RAY DIFFRACTION	r_mcbond_it	0.179	1.5	4047
X-RAY DIFFRACTION	r_mcangle_it	0.346	2	6484
X-RAY DIFFRACTION	r_scbond_it	0.443	3	2538
X-RAY DIFFRACTION	r_scangle_it	0.786	4.5	2447

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.266-2.325	0.287	160	0.246	3372	3572	98.88
2.325-2.388	0.3	191	0.248	3291	3485	99.914
2.388-2.458	0.294	173	0.249	3193	3368	99.941
2.458-2.533	0.284	151	0.245	3128	3280	99.97
2.533-2.616	0.315	170	0.244	2995	3168	99.905
2.616-2.708	0.296	158	0.253	2947	3106	99.968
2.708-2.81	0.283	150	0.252	2792	2946	99.864
2.81-2.925	0.287	162	0.241	2732	2897	99.896
2.925-3.055	0.315	120	0.228	2587	2707	100
3.055-3.204	0.244	135	0.218	2513	2648	100
3.204-3.377	0.272	107	0.206	2393	2501	99.96
3.377-3.581	0.235	120	0.187	2245	2365	100
3.581-3.828	0.213	118	0.182	2104	2222	100
3.828-4.134	0.215	122	0.181	1948	2070	100
4.134-4.528	0.241	90	0.171	1829	1919	100
4.528-5.061	0.191	88	0.178	1643	1731	100
5.061-5.842	0.255	78	0.208	1452	1530	100
5.842-7.148	0.22	71	0.219	1225	1297	99.923
7.148-10.083	0.178	51	0.172	959	1010	100
10.083-99.015	0.213	27	0.195	532	572	97.727

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	0.3506	0.2239	-0.0937	0.6011	-0.1183	0.6364	0.0164	-0.0266	0.0041	-0.0225	-0.0232	-0.0459	-0.0108	-0.0868	0.0068	0.0108	0.0019	-0.0124	0.026	-0.0064	0.0415	31.8318	-25.6625	-20.6204
2	0.3617	-0.0609	0.0643	0.5415	-0.0008	0.7869	0.0584	0.027	0.0377	0.0254	-0.0039	-0.0098	0.0565	-0.0454	-0.0545	0.035	0.0141	-0.0135	0.0144	-0.0054	0.025	41.3109	5.9515	3.958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 410
2	X-RAY DIFFRACTION	1	A	411 - 697
3	X-RAY DIFFRACTION	2	B	4 - 410
4	X-RAY DIFFRACTION	2	B	411 - 701

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