PDB-4l82: Structure of a putative oxidoreductase from Rickettsia felis

ID or keywords:

Entry

Database: PDB / ID: 4l82

Title

Structure of a putative oxidoreductase from Rickettsia felis

Components

RifeA.00250.a

Keywords

OXIDOREDUCTASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID /

National Institute of Allergy and Infectious Diseases

Function / homology

Function and homology information

Biological species

Rickettsia felis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Structure of a putative oxidoreductase from Rickettsia felis
Authors: Clifton, M.C. / Abendroth, J.A.

History

Deposition	Jun 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4l82.cif.gz	260.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4l82.ent.gz	209.9 KB	Display	PDB format
PDBx/mmJSON format	4l82.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l8/4l82 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l82	HTTPS FTP

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Related structure data

Related structure data	1rz1S S: Starting model for refinement
Similar structure data	3fid-2 3uo6-1 3ma6-2 5n48-1 1vju-1 2d36-1 1yoa-1 3unz-2 3uoh-2 5c1v-1 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
Other databases	TargetTrack: SSGCID-RifeA.00250.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: RifeA.00250.a

B: RifeA.00250.a

C: RifeA.00250.a

D: RifeA.00250.a

hetero molecules

76.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RifeA.00250.a

B: RifeA.00250.a

hetero molecules

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

2

C: RifeA.00250.a

D: RifeA.00250.a

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.580, 79.730, 155.140
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	RifeA.00250.a Mass: 18861.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia felis (bacteria) / Strain: ATCC VR-1525 / URRWXCal2 / Gene: RF_1132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4UKE8, Oxidoreductases
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#4: Chemical	ChemComp-SCN / THIOCYANATE ION / Thiocyanate Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.16 Å³/Da / Density % sol: 42.93 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 17 mg/mL RifeA.00250.a, 0.2 M potassium thiocyanate, 20% PEG3350, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL7-1 / Wavelength: 0.97856 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2013

Radiation

Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2→42.941 Å / Num. obs: 44103 / % possible obs: 98 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 28.186 Å² / R_merge(I) obs: 0.095 / Net I/σ(I): 15.07

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2-2.05		0.513	3.77	19659	3182	97.6
2.05-2.11		0.415	4.66	19146	3078	96.1
2.11-2.17		0.369	5.2	18683	3027	97.7
2.17-2.24		0.325	5.8	18298	2971	98.2
2.24-2.31		0.319	6.45	16998	2822	96.1
2.31-2.39		0.249	7.47	17131	2784	97.2
2.39-2.48		0.217	8.45	16635	2695	99
2.48-2.58		0.19	9.58	15948	2607	98.5
2.58-2.7		0.167	10.76	15231	2472	98
2.7-2.83		0.125	13.38	14711	2400	98.3
2.83-2.98		0.098	16.44	14020	2295	98.6
2.98-3.16		0.072	20.68	13232	2170	98.6
3.16-3.38		0.058	24.69	12474	2061	99.1
3.38-3.65		0.047	29.34	11554	1925	99.2
3.65-4		0.041	32.7	10786	1807	99.3
4-4.47		0.04	36.87	9497	1602	99.2
4.47-5.16		0.04	36.83	8160	1435	98.7
5.16-6.32		0.045	32.92	7305	1247	99.1
6.32-8.94		0.042	34.29	5627	993	99.5
	8.94	0.03	44.61	2843	530	87.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZ1

1rz1

Resolution: 2→19.79 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.93 / WR_factor R_free: 0.1994 / WR_factor R_work: 0.1598 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8503 / SU B: 8.224 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1886 / SU R_free: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	2219	5 %	RANDOM
R_work	0.1816	-	-	-
obs	0.184	44048	98 %	-

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 max: 75.83 Å² / B_iso mean: 25.3303 Å² / B_iso min: 11.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	-0 Å²
2-	-	1.94 Å²	0 Å²
3-	-	-	-1.73 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4869	0	51	334	5254

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	5078
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4663
X-RAY DIFFRACTION	r_angle_refined_deg	1.418	1.954	6923
X-RAY DIFFRACTION	r_angle_other_deg	0.767	3	10736
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.796	5	651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.956	25.668	217
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.747	15	809
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.558	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	801
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5854
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1184
X-RAY DIFFRACTION	r_mcbond_it	0.844	1.367	2559
X-RAY DIFFRACTION	r_mcbond_other	0.842	1.364	2555
X-RAY DIFFRACTION	r_mcangle_it	1.392	2.04	3193

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	162	-
R_work	0.21	3012	-
all	-	3174	-
obs	-	-	97.54 %

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	0.5733	0.115	-0.4644	0.1372	-0.5023	2.8914	0.0487	0.0569	0.0777	-0.0028	-0.0182	0.0617	-0.25	0.0174	-0.0305	0.1264	0.007	-0.0025	0.0891	0.0158	0.1179	-19.775	3.89	22.1094
2	2.8556	-3.8644	0.2111	7.8079	-1.0565	2.4976	0.0523	0.1514	-0.0248	-0.0476	-0.1761	0.0973	-0.0013	0.2226	0.1238	0.0643	-0.0134	0.0078	0.0673	0.0092	0.0915	-11.6104	1.3107	26.9309
3	2.2313	0.7126	0.042	1.7577	0.5292	2.9317	0.0344	0.0662	0.0975	-0.0332	0.0032	0.1214	-0.1513	-0.169	-0.0376	0.0719	0.0175	0.0097	0.0393	0.0196	0.052	-25.4431	2.2253	31.9315
4	1.041	0.1527	0.0044	1.0765	-0.1899	2.0833	0.0414	-0.0345	-0.0263	0.0149	-0.0494	0.0055	0.11	0.0007	0.008	0.0404	0.0198	-0.0002	0.0412	0.0072	0.055	-18.4626	-3.6294	28.6153
5	0.8238	0.1342	-0.3484	0.1948	-0.1635	2.5586	-0.064	0.0573	-0.1231	-0.022	-0.0496	-0.1093	0.3458	0.2483	0.1135	0.1152	0.0703	0.0061	0.0728	0.0247	0.0956	-6.7035	-8.531	20.9979
6	3.3401	-1.2295	0.4256	1.5657	-0.3002	2.9322	-0.0398	0.0895	-0.0939	0.1413	-0.0985	0.0288	0.1426	0.3743	0.1383	0.0569	-0.0063	0.0254	0.1343	0.0411	0.0539	-2.9224	-0.2775	16.0417
7	3.2002	1.056	-0.9771	1.9727	-0.4455	2.4577	-0.0522	0.3344	-0.2056	-0.1484	-0.0624	-0.1636	0.3312	0.2435	0.1145	0.1052	0.0977	0.0253	0.14	0.0031	0.0239	-5.2794	-8.1257	3.7139
8	1.7664	0.4932	0.2631	1.1081	-0.4016	2.2102	0.0217	0.069	0.0275	-0.0706	-0.0853	0.0074	0.1609	0.1621	0.0636	0.0732	0.0533	0.0275	0.0567	0.0035	0.0299	-10.351	-3.5764	12.9149
9	5.5884	5.5547	-0.2477	10.9585	-0.9302	3.1985	0.0398	0.0667	0.194	0.0487	0.0217	-0.3238	-0.2417	0.0235	-0.0615	0.0719	0.0127	0.004	0.1134	0.0215	0.0762	3.2148	41.8197	8.4204
10	1.4067	-0.3871	-0.0238	0.8873	-0.0496	1.5159	0.0074	0.0688	0.0948	0.0132	0.0625	0.0043	-0.0935	-0.0138	-0.0699	0.0667	-0.016	0.0091	0.0666	0.0159	0.0748	-13.7365	43.1806	22.1823
11	10.8932	-2.1859	-2.6748	6.9942	6.4344	6.0164	-0.0087	0.0492	0.9906	-0.6748	0.0404	-0.0471	-0.642	-0.0866	-0.0317	0.1206	0.0774	-0.0257	0.2086	0.0214	0.2274	-24.1286	49.4978	19.447
12	1.7701	-0.1628	-0.2607	0.751	0.2601	2.0508	-0.0267	0.1022	-0.0043	0.0222	0.0378	0.0254	0.0374	-0.1042	-0.0111	0.0595	-0.0032	-0.0026	0.0163	0.0143	0.0796	-14.4881	37.3847	20.2711
13	4.296	-1.2821	-2.2616	0.7243	0.6188	1.9613	-0.0289	-0.0592	-0.3526	0.0842	-0.0892	0.0082	0.1831	0.0995	0.1181	0.1399	-0.0061	0.0006	0.0758	0.0296	0.0992	-1.2859	25.4913	18.7593
14	1.769	-1.3692	-0.8299	4.5418	-0.0817	1.9894	-0.006	-0.2091	-0.0119	0.1239	0.0014	0.0345	0.2036	0.3908	0.0045	0.0818	0.0275	-0.0341	0.1769	0.001	0.0325	5.6409	31.9167	22.8537
15	3.793	0.5394	0.6019	1.7434	0.6703	2.3619	-0.0498	0.0388	-0.1796	-0.0597	0.0168	-0.1614	0.2603	0.175	0.0331	0.0776	0.027	0.0369	0.093	0.0299	0.053	8.9254	24.9405	10.1898
16	1.7727	-0.1618	-0.5153	0.9408	-0.0653	3.6637	-0.1118	-0.0457	0.042	-0.0183	0.0246	-0.0394	0.0712	0.0265	0.0872	0.0298	0.0188	0.0113	0.0142	0.0056	0.0531	0.4232	31.6508	14.4937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 38
2	X-RAY DIFFRACTION	2	A	39 - 60
3	X-RAY DIFFRACTION	3	A	61 - 100
4	X-RAY DIFFRACTION	4	A	101 - 160
5	X-RAY DIFFRACTION	5	B	-1 - 38
6	X-RAY DIFFRACTION	6	B	39 - 66
7	X-RAY DIFFRACTION	7	B	67 - 117
8	X-RAY DIFFRACTION	8	B	118 - 160
9	X-RAY DIFFRACTION	9	C	5 - 18
10	X-RAY DIFFRACTION	10	C	19 - 87
11	X-RAY DIFFRACTION	11	C	88 - 101
12	X-RAY DIFFRACTION	12	C	102 - 160
13	X-RAY DIFFRACTION	13	D	5 - 38
14	X-RAY DIFFRACTION	14	D	39 - 68
15	X-RAY DIFFRACTION	15	D	69 - 119
16	X-RAY DIFFRACTION	16	D	120 - 160

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