PDB-3u35: Crystal structure of the general stress FMN/FAD binding protein f...

ID or keywords:

Entry

Database: PDB / ID: 3u35

Title

Crystal structure of the general stress FMN/FAD binding protein from the phytopathogen Xanthomonas citri

Components

General stress protein

Keywords

PROTEIN BINDING / Xanthomonas citri General stress protein FMN binding protein FAD binding protein / PNP-oxidase like fold / FMN/FAD

Function / homology

General stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / TRIETHYLENE GLYCOL / General stress protein

Function and homology information

Biological species

Xanthomonas axonopodis pv. citri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Hilario, E. / Li, Y. / Fan, L.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property.
Authors: Hilario, E. / Li, Y. / Niks, D. / Fan, L.

History

Deposition	Oct 4, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3u35.cif.gz	225.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3u35.ent.gz	184.2 KB	Display	PDB format
PDBx/mmJSON format	3u35.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3u35_validation.pdf.gz	472 KB	Display	wwPDB validaton report
Full document	3u35_full_validation.pdf.gz	480.7 KB	Display
Data in XML	3u35_validation.xml.gz	22.6 KB	Display
Data in CIF	3u35_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/3u35 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u35	HTTPS FTP

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Related structure data

Related structure data	3u34C 1flm 2i02 2ou5 3dmb C: citing same article (ref.)
Similar structure data	3u34-d 4x2m-d 2f98-d 4wx0-d 4ccg-d 3zxu-2 1ici-3 3hl8-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: General stress protein

B: General stress protein

C: General stress protein

D: General stress protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

2

A: General stress protein

D: General stress protein

hetero molecules

defined by author&software
Evidence: gel filtration
40.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: General stress protein

B: General stress protein

hetero molecules

defined by author&software
Evidence: gel filtration
40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

B: General stress protein

C: General stress protein

defined by author&software
Evidence: gel filtration
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

C: General stress protein

D: General stress protein

hetero molecules

defined by author&software
Evidence: gel filtration
40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.204, 122.184, 57.713
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

BASED ON THE SIZE EXCLUSION CHROMATOGRAPHY RESULTS THE PURE RECOMBINANT PROTEIN EXIST AS AN EQUILIBRIUM OF DIMERS AND TETRAMERS IN SOLUTION. HOWEVER, THE AMOUNT OF DIMERIC FORM IS PREDOMINANT WHEN COMPARED WITH THE TETRAMERIC FORM

#1: Protein	General stress protein Mass: 20108.908 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Gene was cloned into EcoRI and HindIII restriction sites of pET28a Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria) Strain: 306 / Gene: General stress protein NCBI-GeneID 1156440, XAC2369 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys-S / References: UniProt: Q8PK08
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.63 Å³/Da / Density % sol: 53.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein concentration at 25mg/mL in 0.1M Hepes, pH 7.5, 42% PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.116 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. all: 30136 / Num. obs: 29232 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / R_merge(I) obs: 0.066 / Net I/σ(I): 24
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.653 / Mean I/σ(I) obs: 2.3 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
Crystal	Clear 2.0 r2	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→19.805 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2392	1511	5.08 %
R_work	0.2012	-	-
obs	0.2031	29232	96.68 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 58.343 Å² / k_sol: 0.379 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	23.6256 Å²	-0 Å²	-0 Å²
2-	-	-15.4536 Å²	-0 Å²
3-	-	-	-8.172 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4263	0	20	46	4329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4377
X-RAY DIFFRACTION	f_angle_d	1.035	5928
X-RAY DIFFRACTION	f_dihedral_angle_d	16.355	1540
X-RAY DIFFRACTION	f_chiral_restr	0.069	648
X-RAY DIFFRACTION	f_plane_restr	0.004	761

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 (%)
2.4819-2.5619	0.3585	145	0.3069	2470	X-RAY DIFFRACTION	95
2.5619-2.6532	0.3029	131	0.2786	2592	X-RAY DIFFRACTION	99
2.6532-2.7592	0.2922	135	0.2658	2591	X-RAY DIFFRACTION	99
2.7592-2.8844	0.2899	138	0.2524	2569	X-RAY DIFFRACTION	99
2.8844-3.036	0.2522	143	0.2264	2568	X-RAY DIFFRACTION	98
3.036-3.2254	0.2733	135	0.2268	2602	X-RAY DIFFRACTION	98
3.2254-3.4732	0.2689	132	0.2163	2548	X-RAY DIFFRACTION	97
3.4732-3.8205	0.2321	135	0.1919	2587	X-RAY DIFFRACTION	97
3.8205-4.3682	0.1978	117	0.169	2588	X-RAY DIFFRACTION	96
4.3682-5.484	0.1977	146	0.162	2548	X-RAY DIFFRACTION	95
5.484-19.8055	0.2251	154	0.1855	2572	X-RAY DIFFRACTION	91

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	0.0176	0.0103	-0.0184	-0.0134	0.0442	0.1074	-0.0698	0.1576	0.0622	-0.474	0.143	0.3004	0.1372	-0.1275	0	0.2859	0.0242	-0.0381	0.3608	0.0041	0.3619	-38.2503	8.6523	-7.2646
2	0.7008	0.4316	-0.1219	0.273	0.221	0.3418	-0.0036	-0.0207	-0.0362	0.0331	0.0917	-0.1952	-0.1474	0.2223	-0	0.3274	0.001	0.0366	0.3336	-0.01	0.317	-20.6213	3.0996	-1.3743
3	0.7263	-0.0989	-0.691	0.638	0.494	0.9985	0.0293	-0.0282	0.0613	-0.2254	0.005	-0.0904	0.0468	-0.0706	-0	0.361	-0.0169	0.0057	0.2561	0.023	0.2548	-23.5271	2.7655	-7.1259
4	0.5202	-0.9121	-0.0567	1.1786	-0.0892	1.0703	0.1329	0.2007	0.0845	-0.5188	-0.1142	-0.2198	-0.1024	0.0533	0	0.4954	-0.0295	0.0956	0.3765	0.0292	0.2469	-17.2771	5.7918	-16.1823
5	0.1014	-0.0891	-0.2043	0.1933	-0.4533	0.3985	0.0817	0.0332	0.0275	0.5745	-0.1311	0.3807	0.2144	-0.2027	0	0.2262	0.0398	0.018	0.3772	-0.019	0.3385	-37.4423	20.1542	11.4029
6	0.0475	0.0196	0.0295	-0.0103	0.0048	0.0768	-0.2186	-0.2531	0.2121	0.9148	0.4613	0.0423	0.4976	0.3103	-0	0.4571	0.0423	-0.0019	0.3229	-0.0516	0.2122	-15.3964	13.6324	15.4344
7	0.8462	0.2351	-0.2138	0.1455	-0.0682	0.1903	-0.0244	-0.1983	-0.0502	0.3306	0.0563	0.1268	0.3022	-0.0944	-0	0.4224	-0.0307	0.0231	0.27	0.0171	0.3331	-29.5416	1.3373	9.3882
8	0.2743	-0.6815	-0.2848	0.3435	-0.0602	0.0792	0.2397	-0.1623	0.1196	0.4161	-0.1666	-0.0457	-0.1528	-0.0956	-0	0.6082	0.0626	0.0363	0.49	0.0038	0.2525	-27.3397	5.4694	21.324
9	-0.027	-0.01	-0.0185	-0.0407	0.0076	-0.0028	-0.0892	1.0018	-0.7302	-0.9434	0.0125	0.3211	0.7347	-0.4523	0	1.2868	-0.0865	-0.0171	0.6273	0.0711	0.572	-34.0432	-9.5103	16.2287
10	0.5938	0.3303	0.2178	-0.1621	-0.048	0.5523	-0.1427	-0.0842	0.0122	0.1769	0.0663	-0.1178	0.3437	0.0953	-0	0.5622	0.0912	0.0715	0.2822	-0.003	0.23	-24.9308	2.5684	16.344
11	0.1149	-0.2157	0.0209	0.0359	0.1283	0.1413	-0.4722	0.0576	-0.0062	0.6735	0.4471	0.4581	-0.6477	-0.6942	0	0.5192	0.0083	0.1195	0.6545	0.0968	0.4187	-40.4479	4.2578	24.214
12	0.3966	0.0746	0.0915	0.09	0.3741	0.2046	-0.1877	-0.3247	0.1681	-0.2363	0.1701	0.029	0.9421	0.5017	-0	0.5036	0.1009	-0.0407	0.4526	0.0693	0.371	-18.8039	2.7874	13.8733
13	-0.0069	-0.1016	-0.077	0.067	0.1469	0.1762	0.071	0.2645	0.2891	-0.1335	-0.5583	-0.5398	0.3371	0.1626	-0	0.4891	0.033	0.1369	0.6254	0.0951	0.6056	-20.9066	32.2132	-5.9844
14	0.4614	-0.333	0.6496	0.6612	0.144	0.2566	0.1897	-0.0058	-0.4749	-0.389	-0.3358	-0.092	-0.6167	0.2143	-0	0.3002	0.023	-0.0056	0.2026	-0.0249	0.1933	-30.7549	27.801	-9.2828
15	0.4296	0.0613	-0.3934	0.0996	-0.2452	0.1155	-0.0211	0.0698	0.0422	0.0811	0.14	0.2359	-0.1982	-0.051	0	0.3348	-0.029	0.0124	0.3126	0.0136	0.359	-39.3212	35.9424	4.0254
16	1.236	0.1076	0.7287	0.6861	0.1486	0.6878	-0.0621	0.0693	0.1393	0.0474	0.002	0.1943	0.145	-0.0166	0	0.1595	-0.0406	0.0198	0.1736	0.0195	0.2412	-38.9269	36.3936	-0.9688
17	0.9243	0.2245	0.4392	0.5661	0.2697	0.8935	-0.0018	-0.0397	-0.0317	-0.1521	-0.026	0.1822	0.0555	-0.12	-0	0.3892	-0.05	-0.0648	0.4523	0.0081	0.575	-49.3246	31.7779	-3.3893
18	-0.8631	-0.8072	-0.0633	-0.2883	-0.4213	-0.402	0.9483	0.5078	-1.1481	0.4933	0.0451	-1.5162	0.2098	0.9082	0	0.1188	0.0906	0.3329	0.2955	0.1445	-0.3101	-15.6599	18.3405	2.1061
19	0.2896	-0.3243	0.2744	0.2548	-0.0464	0.0449	-0.0427	-0.0565	0.0476	0.0231	0.1193	-0.1067	0.191	-0.1503	-0	0.3821	0.0287	-0.0465	0.2471	0.0057	0.2975	-25.7339	27.1821	16.0931
20	0.4169	0.2171	-0.1431	0.2805	0.1052	0.1267	-0.2176	0.1332	0.3005	0.4563	-0.0457	-0.2361	-0.7983	0.3046	-0	0.3645	-0.0159	-0.0043	0.2554	-0.0039	0.3547	-22.1353	39.7678	6.6618
21	1.8753	-0.4021	-0.1224	0.3875	-0.1652	0.7546	0.0307	-0.2562	0.3002	0.2407	-0.0168	-0.0844	0.0949	-0.0118	0	0.149	0.034	-0.0213	0.2898	-0.0598	0.3465	-22.6403	38.2585	11.3917
22	0.8326	0.1142	0.0326	0.2332	-0.2233	0.4449	0.084	-0.1576	-0.1581	0.0908	0.0221	-0.2646	-0.0358	0.0527	-0	0.3653	0.0372	-0.1168	0.5979	-0.0148	0.7904	-6.8971	37.3782	11.4717
23	-0.0161	-1.0961	-1.1306	0.9122	-0.6832	0.0262	-0.039	-0.089	0.0895	0.2404	-0.0872	0.308	0.054	-0.0821	0	0.2853	-0.0189	0.0064	0.405	-0.0064	0.3344	-32.4573	23.7211	10.5851

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 24:34)
2	X-RAY DIFFRACTION	2	(chain A and resid 35:54)
3	X-RAY DIFFRACTION	3	(chain A and resid 55:107)
4	X-RAY DIFFRACTION	4	(chain A and resid 108:147)
5	X-RAY DIFFRACTION	5	(chain A and resid 148:165)
6	X-RAY DIFFRACTION	6	(chain B and resid 24:34)
7	X-RAY DIFFRACTION	7	(chain B and resid 35:56)
8	X-RAY DIFFRACTION	8	(chain B and resid 57:73)
9	X-RAY DIFFRACTION	9	(chain B and resid 74:83)
10	X-RAY DIFFRACTION	10	(chain B and resid 84:118)
11	X-RAY DIFFRACTION	11	(chain B and resid 119:138)
12	X-RAY DIFFRACTION	12	(chain B and resid 139:151)
13	X-RAY DIFFRACTION	13	(chain B and resid 152:164)
14	X-RAY DIFFRACTION	14	(chain C and resid 23:40)
15	X-RAY DIFFRACTION	15	(chain C and resid 41:62)
16	X-RAY DIFFRACTION	16	(chain C and resid 63:107)
17	X-RAY DIFFRACTION	17	(chain C and resid 108:148)
18	X-RAY DIFFRACTION	18	(chain C and resid 149:164)
19	X-RAY DIFFRACTION	19	(chain D and resid 24:42)
20	X-RAY DIFFRACTION	20	(chain D and resid 43:62)
21	X-RAY DIFFRACTION	21	(chain D and resid 63:107)
22	X-RAY DIFFRACTION	22	(chain D and resid 108:137)
23	X-RAY DIFFRACTION	23	(chain D and resid 138:164)

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