PDB-3l20: Crystal structure of a hypothetical protein from Staphylococcus aureus

ID or keywords:

Entry

Database: PDB / ID: 3l20

Title

Crystal structure of a hypothetical protein from Staphylococcus aureus

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION / hypothetical protein

Function / homology

PhnB-like / 3-demethylubiquinone-9 3-methyltransferase / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / 3-dmu-9_3-mt domain-containing protein / 3-dmu-9_3-mt domain-containing protein

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.451 Å

Authors

Lam, R. / Chan, T. / Battaile, K.P. / Mihajlovic, V. / Romanov, V. / Soloveychik, M. / Kisselman, G. / McGrath, T.E. / Lam, K. / Pai, E.F. / Chirgadze, N.Y.

Citation

Journal: To be Published
Title: Crystal structure of a hypothetical protein from Staphylococcus aureus
Authors: Lam, R. / Chan, T. / Battaile, K.P. / Mihajlovic, V. / Romanov, V. / Pai, E.F. / Chirgadze, N.Y.

History

Deposition	Dec 14, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3l20.cif.gz	70.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3l20.ent.gz	55.5 KB	Display	PDB format
PDBx/mmJSON format	3l20.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l20_validation.pdf.gz	438.1 KB	Display	wwPDB validaton report
Full document	3l20_full_validation.pdf.gz	439.8 KB	Display
Data in XML	3l20_validation.xml.gz	12.6 KB	Display
Data in CIF	3l20_validation.cif.gz	16.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/3l20 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l20	HTTPS FTP

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Related structure data

Similar structure data	2nol-d 4a69-2 3jsi-1 6lvs-6 2ges-d 1k30-d 1zho-1 3ktu-d 1yqr-d 5xls-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	91.668, 93.027, 94.453
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#1: Protein	Putative uncharacterized protein Mass: 19897.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: SAUSA300_2529 / Plasmid: pW2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: Q2FDR5, UniProt: A0A0H2XH33*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative uncharacterized protein

Mass: 19897.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: SAUSA300_2529 / Plasmid: pW2 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: Q2FDR5, UniProt: A0A0H2XH33*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.53 Å³/Da / Density % sol: 51.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 15% PEG3350, 0.2M Mg acetate, 3% ethanol, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 0.97928 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 23, 2008 / Details: Si(111) double-crystal monochromator

Radiation

Monochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97928 Å / Relative weight: 1

Reflection

Resolution: 2.45→50 Å / Num. obs: 15138 / % possible obs: 99.7 % / Redundancy: 7.3 % / R_merge(I) obs: 0.09 / Χ²: 1.154 / Net I/σ(I): 9.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.45-2.54	7.2	0.485	1476	0.882	99.4
2.54-2.64	7.4	0.377	1488	0.899	99.7
2.64-2.76	7.4	0.293	1496	0.969	99.5
2.76-2.9	7.4	0.226	1496	0.973	99.8
2.9-3.09	7.4	0.161	1500	1.095	99.8
3.09-3.32	7.3	0.102	1504	1.168	99.8
3.32-3.66	7.3	0.078	1517	1.159	99.9
3.66-4.19	7.3	0.064	1510	1.192	99.8
4.19-5.28	7.2	0.052	1539	1.352	99.6
5.28-50	6.7	0.058	1612	1.875	99.3

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.45 Å / D res low: 32.65 Å / FOM acentric: 0.265 / FOM centric: 0.057 / Reflection acentric: 13397 / Reflection centric: 1640

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	2.45	32.65	13397	1640
ANO_1	0.874	0	2.45	32.65	13373	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	10.41-32.65	0	140	83
ISO_1	7.56-10.41	0	263	81
ISO_1	6.23-7.56	0	337	85
ISO_1	5.42-6.23	0	412	85
ISO_1	4.86-5.42	0	476	83
ISO_1	4.44-4.86	0	512	78
ISO_1	4.12-4.44	0	572	80
ISO_1	3.86-4.12	0	603	82
ISO_1	3.64-3.86	0	654	83
ISO_1	3.46-3.64	0	702	81
ISO_1	3.3-3.46	0	744	80
ISO_1	3.16-3.3	0	767	84
ISO_1	3.03-3.16	0	803	87
ISO_1	2.92-3.03	0	833	85
ISO_1	2.83-2.92	0	859	79
ISO_1	2.74-2.83	0	876	79
ISO_1	2.66-2.74	0	919	83
ISO_1	2.58-2.66	0	953	85
ISO_1	2.51-2.58	0	963	79
ISO_1	2.45-2.51	0	1009	78
ANO_1	10.41-32.65	0.441	140	0
ANO_1	7.56-10.41	0.406	262	0
ANO_1	6.23-7.56	0.439	337	0
ANO_1	5.42-6.23	0.496	412	0
ANO_1	4.86-5.42	0.605	476	0
ANO_1	4.44-4.86	0.66	512	0
ANO_1	4.12-4.44	0.751	572	0
ANO_1	3.86-4.12	0.819	603	0
ANO_1	3.64-3.86	0.856	653	0
ANO_1	3.46-3.64	0.848	702	0
ANO_1	3.3-3.46	0.888	744	0
ANO_1	3.16-3.3	0.907	767	0
ANO_1	3.03-3.16	0.926	802	0
ANO_1	2.92-3.03	0.963	832	0
ANO_1	2.83-2.92	0.964	857	0
ANO_1	2.74-2.83	0.977	875	0
ANO_1	2.66-2.74	0.984	917	0
ANO_1	2.58-2.66	0.994	950	0
ANO_1	2.51-2.58	0.995	960	0
ANO_1	2.45-2.51	0.997	1000	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-20.46	-0.848	-21.836	SE	37.26	0.48
2	-20.132	-20.804	-24.239	SE	41.66	0.49
3	-16.391	9.946	-30.537	SE	33.47	0.31
4	-22.988	15.01	-32.457	SE	63.86	0.46
5	-29.536	15.803	-38.812	SE	68.85	0.41
6	-7.428	8.678	-31.504	SE	48.94	0.31
7	-24.384	4.837	-22.196	SE	46.42	0.16
8	-22.866	-25.426	-26.85	SE	40.54	0.28
9	-40.538	-6.755	-25.068	SE	224.8	0.7
10	-37.778	-15.922	-33.702	SE	208.89	0.45
11	-43.057	-1.071	-61.379	SE	185.35	0.44

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
10.41-32.65	0.529	0.103	140	83
7.56-10.41	0.562	0.079	263	81
6.23-7.56	0.552	0.072	337	85
5.42-6.23	0.526	0.087	412	85
4.86-5.42	0.438	0.066	476	83
4.44-4.86	0.428	0.062	512	78
4.12-4.44	0.389	0.041	572	80
3.86-4.12	0.326	0.047	603	82
3.64-3.86	0.316	0.042	654	83
3.46-3.64	0.313	0.037	702	81
3.3-3.46	0.292	0.051	744	80
3.16-3.3	0.28	0.048	767	84
3.03-3.16	0.252	0.049	803	87
2.92-3.03	0.207	0.042	833	85
2.83-2.92	0.196	0.062	859	79
2.74-2.83	0.175	0.048	876	79
2.66-2.74	0.163	0.06	919	83
2.58-2.66	0.142	0.051	953	85
2.51-2.58	0.129	0.046	963	79
2.45-2.51	0.111	0.048	1009	78

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 15037

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.86-100	66.2	0.778	505
6.18-7.86	65.9	0.84	504
5.38-6.18	63.6	0.864	508
4.88-5.38	64.6	0.897	502
4.51-4.88	57.2	0.933	510
4.23-4.51	66.6	0.919	510
4.01-4.23	64.8	0.924	510
3.83-4.01	66.3	0.905	504
3.68-3.83	69.1	0.898	510
3.55-3.68	66.6	0.906	525
3.43-3.55	73.2	0.894	550
3.32-3.43	73.9	0.921	550
3.22-3.32	75	0.914	581
3.13-3.22	75.7	0.884	595
3.04-3.13	74.1	0.852	611
2.97-3.04	82.7	0.828	621
2.9-2.97	83.7	0.831	630
2.83-2.9	80.6	0.837	645
2.77-2.83	77.9	0.818	652
2.71-2.77	80.4	0.809	676
2.65-2.71	79.9	0.826	694
2.6-2.65	86.6	0.832	696
2.55-2.6	82.5	0.796	724
2.51-2.55	86.1	0.775	721
2.45-2.51	87.5	0.679	1003

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.005	data extraction
JDirector		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.451→19.834 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.929 / WR_factor R_free: 0.226 / WR_factor R_work: 0.197 / ESU R: 0.382 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.237	752	5.011 %
R_work	0.2089	-	-
obs	-	15007	99.036 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.422 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.065 Å²	0 Å²	0 Å²
2-	-	-0.073 Å²	0 Å²
3-	-	-	0.008 Å²

Refinement step

Cycle: LAST / Resolution: 2.451→19.834 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2402	0	0	28	2430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2458
X-RAY DIFFRACTION	r_angle_refined_deg	1.528	1.932	3312
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.299	5	297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.567	25.338	133
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.767	15	417
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.54	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	340
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1911
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	863
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	1646
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	64
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.174	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.092	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.762	1.5	1474
X-RAY DIFFRACTION	r_mcangle_it	1.531	2	2348
X-RAY DIFFRACTION	r_scbond_it	2.368	3	984
X-RAY DIFFRACTION	r_scangle_it	3.99	4.5	964

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 (%)
2.451-2.513	0.381	47	0.238	1034	1098	98.452
2.513-2.581	0.266	40	0.226	998	1051	98.763
2.581-2.654	0.301	64	0.239	956	1033	98.742
2.654-2.735	0.316	43	0.246	951	1004	99.004
2.735-2.823	0.302	45	0.257	901	967	97.828
2.823-2.919	0.32	53	0.236	879	949	98.209
2.919-3.027	0.327	46	0.234	868	921	99.24
3.027-3.148	0.305	42	0.214	848	892	99.776
3.148-3.284	0.258	35	0.224	801	837	99.881
3.284-3.439	0.294	47	0.216	762	812	99.631
3.439-3.62	0.225	38	0.201	738	780	99.487
3.62-3.831	0.226	32	0.215	723	755	100
3.831-4.085	0.219	30	0.196	642	684	98.246
4.085-4.397	0.167	38	0.177	613	659	98.786
4.397-4.793	0.153	30	0.156	562	605	97.851
4.793-5.32	0.183	52	0.185	507	561	99.643
5.32-6.07	0.303	32	0.228	469	501	100
6.07-7.266	0.228	18	0.222	423	441	100
7.266-9.649	0.136	14	0.193	336	351	99.715
9.649-19.834	0.176	6	0.195	244	252	99.206

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	0.6952	-0.1957	-0.3827	3.8042	0.3666	0.924	0.047	0.092	0.0024	-0.5602	-0.0286	-0.1464	-0.0869	0.0039	-0.0184	0.1123	0.0252	0.048	0.0337	0.0251	0.0455	25.882	35.292	14.899
2	0.6503	-0.2396	0.0306	4.6016	0.1759	1.623	-0.0121	0.03	-0.0617	0.4737	-0.0407	0.0947	0.1021	-0.0479	0.0528	0.0859	-0.0306	0.0302	0.0249	-0.0123	0.0369	20.813	35.94	32.954

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	-2 - 151
2	X-RAY DIFFRACTION	2	ALL	B	3 - 147

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