PDB-3sxz: Metal-free FCD domain of TM0439 a putative transcriptional regulator

ID or keywords:

Entry

Database: PDB / ID: 3sxz

Title

Metal-free FCD domain of TM0439 a putative transcriptional regulator

Components

Transcriptional regulator, GntR family

Keywords

TRANSCRIPTION REGULATOR / TRANSCRIPTION FACTOR / TRANSCRIPTION / METAL-BINDING / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / FADR-C / FADR / GNTR / TRANSCRIPTIONAL REGULATOR / TRANSCRIPTION REPRESSOR / ZINC-BINDING / NICKEL-BINDING / DNA-BINDING / SURFACE ENTROPY REDUCTION

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.322 Å

Authors

Czelakowski, G.P. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)

Citation

Journal: To be Published
Title: Metal-free FCD domain of TM0439 a putative transcriptional regulator
Authors: Czelakowski, G.P. / Derewenda, Z.S.

History

Deposition	Jul 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 13, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3sxz.cif.gz	131.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3sxz.ent.gz	104.6 KB	Display	PDB format
PDBx/mmJSON format	3sxz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3sxz_validation.pdf.gz	427.9 KB	Display	wwPDB validaton report
Full document	3sxz_full_validation.pdf.gz	429.3 KB	Display
Data in XML	3sxz_validation.xml.gz	12.3 KB	Display
Data in CIF	3sxz_validation.cif.gz	16.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxz ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxz	HTTPS FTP

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Related structure data

Related structure data	3sxmC 3fmsS 3sxk 3sxy S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4gok-1 4llo-3 3ewi-d 6x9n-1 5no6-1 3v0g-4 6x9f-8 3sxk-d 1ne4-d 5no6-2 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	TargetDB: ISFI335

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, GntR family

B: Transcriptional regulator, GntR family

33.3 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)	80.890, 80.890, 91.739
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain 'A' and (resseq 72:117 or resseq 123:211 )	A	0
2	1	1	chain 'B' and (resseq 72:117 or resseq 123:211 )	B	0

NCS oper: (Code: given
Matrix: (-0.775357, -0.129024, 0.618202), (-0.127235, -0.926918, -0.353036), (0.618573, -0.352386, 0.702276)
Vector: -9.74146, 101.407997, 24.4641)

Details

biological unit is the same as asym.

#1: Protein	Transcriptional regulator, GntR family Mass: 16633.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0439 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYS0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.6 Å³/Da / Density % sol: 52.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50 mM Tris pH 8.0, 100 mM NaCl, 1M tri-sodium citrate, 0.1M sodium cacodylate pH 6.5, 10 mM EDTA, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 93 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 3, 2009

Radiation

Monochromator: Confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.32→42 Å / Num. all: 15582 / Num. obs: 15441 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / B_iso Wilson estimate: 37.7 Å² / R_merge(I) obs: 0.091 / Χ²: 0.994 / Net I/σ(I): 14.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.32-2.36	4.6	0.533	746	1.123	1	98.4
2.36-2.4	5.4	0.512	763	1.026	1	100
2.4-2.45	6.5	0.431	768	1.008	1	100
2.45-2.5	6.6	0.388	754	1.005	1	100
2.5-2.55	6.7	0.368	748	1.003	1	100
2.55-2.61	6.6	0.315	774	0.991	1	100
2.61-2.68	6.7	0.274	757	0.946	1	100
2.68-2.75	6.7	0.242	748	1.06	1	100
2.75-2.83	6.7	0.206	768	1.02	1	100
2.83-2.92	6.7	0.162	762	1.007	1	100
2.92-3.03	6.7	0.134	761	0.993	1	100
3.03-3.15	6.7	0.11	775	0.978	1	100
3.15-3.29	6.7	0.095	777	0.954	1	100
3.29-3.47	6.7	0.076	756	1.002	1	100
3.47-3.68	6.6	0.071	781	0.97	1	100
3.68-3.97	6.7	0.06	784	0.97	1	100
3.97-4.37	6.6	0.056	787	0.938	1	100
4.37-5	6.5	0.055	785	0.922	1	100
5-6.29	6.4	0.06	797	1.03	1	99.9
6.29-42	5.8	0.049	850	0.988	1	98.6

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	dev_817	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb: 3fms, Chain A, 72-211

3fms

Resolution: 2.322→27.838 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8313 / SU ML: 0.45 / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2277	1025	6.65 %	SCALEPACK2MTZ FREERFRAC 0.05, RANDOM
R_work	0.1968	-	-	-
obs	0.1989	15410	99.86 %	-
all	-	15441	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.216 Å² / k_sol: 0.409 e/Å³

Displacement parameters

B_iso max: 137.3 Å² / B_iso mean: 45.2134 Å² / B_iso min: 16.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.158 Å²	-0 Å²	-0 Å²
2-	-	5.158 Å²	0 Å²
3-	-	-	-10.3159 Å²

Refinement step

Cycle: LAST / Resolution: 2.322→27.838 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2327	0	0	71	2398

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2366
X-RAY DIFFRACTION	f_angle_d	1.081	3167
X-RAY DIFFRACTION	f_chiral_restr	0.069	348
X-RAY DIFFRACTION	f_plane_restr	0.005	409
X-RAY DIFFRACTION	f_dihedral_angle_d	16.989	929

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1121	X-RAY DIFFRACTION	POSITIONAL	0.731
1	2	B	1121	X-RAY DIFFRACTION	POSITIONAL	0.731

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3216-2.4439	0.2839	136	0.249	2020	2156	99
2.4439-2.5969	0.2999	168	0.2409	1995	2163	100
2.5969-2.7973	0.2615	145	0.2376	2036	2181	100
2.7973-3.0785	0.2629	141	0.2224	2030	2171	100
3.0785-3.5232	0.2496	142	0.2067	2072	2214	100
3.5232-4.4359	0.1907	129	0.1598	2075	2204	100
4.4359-27.8402	0.1909	164	0.1783	2157	2321	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	0.6826	0.7199	0.4974	0.5483	0.3747	0.2166	0.0003	-0.0809	0.0364	-0.1721	0.0896	0.0435	-0.0056	0.0835	0	0.2864	0.0345	0.0365	0.1921	-0.0186	0.2372	-1.3782	58.6335	9.9715
2	0.5894	0.1164	-0.0301	0.0888	0.0274	0.0588	0.3172	0.0902	0.0869	-0.1816	-0.0554	0.0114	0.2945	0.2156	0.1012	0.4206	0.0988	0.0219	0.1707	0.0167	0.2885	8.7461	40.4087	11.2065
3	1.2371	2.3258	0.4137	4.5329	0.7442	0.253	-0.1927	0.5424	0.0835	-1.5516	0.5856	-0.6313	-0.2098	0.5385	-0.007	0.4907	0.1967	0.0914	0.5644	-0.0715	0.3602	19.1492	47.8249	3.9791
4	0.3776	0.3272	-0.0985	0.1381	-0.0493	0.4759	0.0936	0.4586	-0.2904	-0.4995	-0.19	-0.2422	0.0005	0.0591	-0.0181	0.363	0.101	0.1243	0.2727	0.0575	0.2906	12.0353	53.5718	2.3095
5	1.5777	0.7812	-0.2581	0.6316	-0.6573	0.7453	-0.0189	1.1348	-0.1021	-0.8121	0.0958	-0.0903	-0.0345	-0.3612	-0.0354	0.4497	0.0777	0.0614	0.2437	0.1008	0.2267	0.3372	56.3643	0.7872
6	1.0559	0.7853	0.3743	1.2589	0.1511	1.2659	0.0491	0.2027	0.1486	0.4203	0.0287	-0.2823	-0.1396	0.7977	0.2266	0.2343	0.0448	0.0345	0.3368	0.0889	0.347	16.1967	55.9588	12.1757
7	0.406	-0.7777	0.0679	0.9331	0.089	0.0911	-0.213	0.0127	0.2478	0.5513	-0.0331	-0.7788	-0.2251	0.2504	-0.0204	0.3442	-0.0044	-0.0464	0.1682	0.0153	0.3167	7.2315	63.2534	13.473
8	0.4697	0.6405	-0.4156	0.5859	-0.4031	0.2625	-0.079	-0.0168	-0.0817	-0.2638	0.1255	0.0894	0.004	-0.1126	-0	0.2784	-0.0083	-0.0384	0.2103	0.0167	0.3209	-10.0359	43.6658	10.1489
9	0.0858	-0.0935	-0.0503	0.148	0.1344	0.1402	0.4925	-0.5044	0.4512	-0.2267	-0.0929	0.1731	-0.4522	0.0915	0.005	0.2682	-0.0033	-0.0242	0.308	-0.0288	0.2633	-14.7533	58.8265	23.616
10	0.2743	0.2567	0.155	0.6357	-0.5172	1.1845	0.1382	0.4535	0.6148	0.1782	0.1495	1.1409	-0.2272	-1.11	0.2214	0.2092	0.0976	0.0107	0.6022	0.0558	0.395	-28.4944	52.4307	22.1403
11	0.0096	-0.0108	-0.0099	0.0496	-0.0164	0.0164	-0.2766	0.4027	-0.3674	-0.2772	0.1237	-0.2478	-0.0774	-0.087	-0.0001	0.4622	-0.1399	0.024	1.0413	0.1301	0.4011	-35.2131	41.5989	20.2396
12	0.5818	0.1641	-0.2593	0.2274	0.0672	0.2797	-0.0585	0.0899	0.345	0.0078	0.0922	-0.0256	-0.0197	-0.6056	0.0384	0.2895	0.0334	-0.0217	0.4637	0.0352	0.2456	-23.0888	50.3977	13.9876
13	0.3022	0.0047	-0.0372	0.2385	0.481	0.9901	0.3684	0.3204	-0.0044	0.3915	-0.3406	0.2563	0.1442	-0.3727	-0.0717	0.3715	0.0664	-0.027	0.1766	-0.0088	0.2509	-12.5143	56.2321	6.5103
14	0.1822	0.0696	-0.0343	0.62	-0.2734	1.457	-0.1283	0.0161	-0.0263	-0.2573	0.3314	0.2554	0.2713	-1.2066	0.029	0.261	-0.0541	-0.0988	0.3896	-0.0776	0.3072	-21.3481	40.6224	7.2874
15	0.3311	-0.3275	-0.5033	0.4275	0.5038	0.5611	0.3795	-0.6146	0.0045	0.3478	-0.2881	0.0547	0.3231	-0.7479	0.0294	0.2475	-0.0998	-0.0058	0.4757	0.0144	0.2672	-21.5264	44.7271	25.1571
16	0.1491	0.1076	-0.2936	0.8959	0.554	1.0791	0.1528	-0.2271	0.0257	0.8878	-0.2536	-0.1137	0.9057	-0.5412	-0.009	0.2258	-0.0506	-0.0028	0.2299	0.0207	0.2705	-13.8029	39.7872	19.1408
17	0.2564	-0.0013	-0.1695	0.4362	-0.2585	1.5467	-0.6507	0.4268	-0.0128	-0.8201	-0.0008	-0.6538	-0.3104	0.6272	-0.1162	0.6783	-0.3154	0.16	0.5355	-0.0789	0.467	-19.9507	27.6228	4.8773

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 72:96)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 97:104)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 105:116)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 117:143)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 144:163)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 164:185)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 186:211)	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 72:96)	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 97:104)	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 105:117)	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 118:122)	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 123:141)	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 142:153)	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 154:166)	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 167:185)	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 186:206)	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 207:211)	B

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