PDB-3mzy: The Crystal Structure of the RNA polymerase sigma-H factor from F...

ID or keywords:

Entry

Database: PDB / ID: 3mzy

Title

The Crystal Structure of the RNA polymerase sigma-H factor from Fusobacterium nucleatum to 2.5A

Components

RNA polymerase sigma-H factor

Keywords

RNA BINDING PROTEIN / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

sigma factor activity / DNA-templated transcription initiation / regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Fusobacterium nucleatum subsp. nucleatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Stein, A.J. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of the RNA polymerase sigma-H factor from Fusobacterium nucleatum to 2.5A
Authors: Stein, A.J. / Chhor, G. / Clancy, S. / Joachimiak, A.

History

Deposition	May 13, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mzy.cif.gz	65.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3mzy.ent.gz	49.5 KB	Display	PDB format
PDBx/mmJSON format	3mzy.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/mz/3mzy ftp://data.pdbj.org/pub/pdb/validation_reports/mz/3mzy	HTTPS FTP

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Related structure data

Similar structure data	2kjk-d 1wyr-d 2jph-d 1jpc-d 2ys3-d 4dip-8 2rqh-d 5enu-1 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: APC66349.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (5)

Deposited unit

A: RNA polymerase sigma-H factor

19.4 kDa, 1 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)	71.761, 71.761, 153.623
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	RNA polymerase sigma-H factor Mass: 19359.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria) Strain: ATCC 25586 / Gene: FN1518 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RIQ2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.29 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 1000, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.5→50 Å / Num. obs: 8730 / % possible obs: 99.9 % / Redundancy: 14.4 % / R_merge(I) obs: 0.083 / Χ²: 1.631 / Net I/σ(I): 9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.5-2.59	14.7	0.599	836	0.828	100
2.59-2.69	14.8	0.442	849	0.856	100
2.69-2.82	14.5	0.332	843	0.915	100
2.82-2.96	14.4	0.226	849	0.994	100
2.96-3.15	14.4	0.177	850	1.104	100
3.15-3.39	14.4	0.121	864	1.302	100
3.39-3.73	14.3	0.09	857	1.788	100
3.73-4.27	14.4	0.074	884	2.302	100
4.27-5.38	14.8	0.066	899	2.596	100
5.38-50	13.6	0.057	999	3.37	99.4

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.5→31.07 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.904 / SU B: 17.069 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.269	412	4.7 %	RANDOM
R_work	0.234	-	-	-
obs	0.236	8675	99.79 %	-

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 mean: 62.632 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.04 Å²	-0.02 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→31.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	971	0	0	12	983

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	984
X-RAY DIFFRACTION	r_angle_refined_deg	1.138	1.962	1323
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.628	5	121
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.403	24.348	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.983	15	179
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.128	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	152
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	724
X-RAY DIFFRACTION	r_mcbond_it	0.374	1.5	610
X-RAY DIFFRACTION	r_mcangle_it	0.722	2	969
X-RAY DIFFRACTION	r_scbond_it	1.314	3	374
X-RAY DIFFRACTION	r_scangle_it	2.1	4.5	354

LS refinement shell

Resolution: 2.498→2.562 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	36	-
R_work	0.248	580	-
all	-	616	-
obs	-	-	98.25 %

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	36.1768	46.2923	-26.7248	54.0243	-35.0343	27.0077	1.631	0.8117	3.2164	2.3184	1.2797	4.4723	-1.9442	-2.7712	-2.9106	0.7387	0.0466	0.2868	1.0422	-0.423	1.31	0.866	50.5039	17.8329
2	4.8166	0.0403	-4.3001	-0.0495	0.2365	2.5935	0.3997	-0.5734	0.1655	0.3414	-0.169	-0.2017	-0.3567	0.4073	-0.2307	0.9032	-0.274	-0.1667	0.3438	0.096	0.5366	12.132	52.3679	17.4557
3	7.4922	-2.68	0.3234	23.8729	-6.4721	8.0586	-0.0146	-0.9129	-0.0742	0.4269	0.5165	-2.0465	0.6581	1.6709	-0.5019	0.6422	-0.0388	-0.1933	1.1324	-0.0532	0.8164	24.0307	47.8269	16.9253
4	29.7939	7.6684	22.9816	5.4263	1.8466	21.4232	-0.2748	0.6958	-0.9104	-0.1054	-0.1007	-0.9461	0.0662	1.1312	0.3754	0.4981	0.0922	0.2135	0.4036	0.2509	0.7274	18.4052	45.3235	12.636
5	6.9117	8.9587	10.8926	10.611	13.6961	17.326	0.6317	-0.1349	-0.578	0.8421	-0.09	-0.7081	0.9917	0.3049	-0.5417	0.4251	-0.0786	-0.0192	0.4313	0.2193	0.567	11.006	42.7602	16.5845
6	25.653	12.7807	-7.7534	39.3449	-19.3376	8.7261	0.6899	-1.1722	0.1874	1.8928	-0.7456	0.0856	-0.9358	0.3895	0.0556	0.6357	-0.0792	0.077	0.4489	-0.0409	0.5321	3.9302	43.1795	24.255
7	12.8702	14.468	0.3364	21.7243	12.2887	19.1085	-0.3656	1.3113	0.4883	0.3723	1.0246	0.164	0.1054	-0.9362	-0.659	1.1328	0.2682	0.0152	0.9645	0.041	0.9739	0.0956	49.3834	30.6096
8	17.1134	11.913	-21.5187	24.3463	17.2489	75.8473	0.8213	-0.3127	0.3705	0.7846	-0.1696	0.3338	-0.3327	0.0857	-0.6517	0.6066	-0.0859	0.0831	0.4901	0.0715	0.6317	5.7767	62.249	25.0043
9	4.4497	-11.0842	-10.984	19.3447	-0.4084	74.2031	-0.3847	0.0966	0.419	0.4824	-0.584	-0.7839	0.4878	0.4634	0.9688	0.4471	-0.1673	-0.0212	0.3392	-0.0314	0.6576	7.2252	60.7458	16.6523
10	4.0296	-3.3664	-6.8349	9.4372	-5.8582	30.7958	0.0001	0.4343	-0.1986	-0.0133	0.1787	0.4771	-0.1013	-1.6484	-0.1788	0.3356	0.007	0.0337	0.2471	-0.0006	0.3574	7.1086	62.1733	8.0452
11	5.2911	3.1718	-6.9647	27.6085	9.2284	14.6399	-0.2353	0.0829	-0.0263	-0.9448	-0.0761	0.3252	0.015	-0.212	0.3115	0.3251	-0.0002	0.0519	0.1994	0.0303	0.3474	9.5502	55.5788	0.4611
12	17.25	-1.4774	0.7451	11.9193	-9.1313	20.2689	-0.3342	1.0534	-0.2897	0.0908	0.204	1.0111	0.4494	-0.8224	0.1302	0.3002	-0.0443	-0.0528	0.2038	0.0154	0.3465	6.4967	51.9562	4.0502
13	-0.3386	0.0786	0.1829	11.6004	-11.6363	10.8564	0.0523	-0.0436	0.0138	-0.158	0.2701	0.3803	0.2558	-0.2661	-0.3224	0.3945	-0.0628	0.0285	0.2883	0.0042	0.3345	5.2947	46.9788	9.2622
14	30.0411	5.611	-8.8119	12.9159	-2.5635	13.8527	0.3617	-0.6549	-1.0374	-0.7898	-0.4937	-1.135	0.7155	1.1634	0.132	0.3519	-0.0073	0.0194	0.2275	0.0438	0.3683	11.1439	40.0172	6.0654
15	10.1672	-2.3164	1.0838	11.9026	-0.4546	-0.7029	-0.0617	0.1283	-0.4088	-0.4964	0.1599	0.3861	0.0323	-0.0467	-0.0983	0.408	-0.0706	0.0217	0.2818	0.0491	0.3616	7.5345	41.6314	0.537
16	23.0278	23.5356	5.3676	21.3948	5.8879	11.1059	-0.5194	0.0558	-0.8606	-0.5466	-0.045	-0.8543	0.1973	0.4229	0.5644	0.5104	0.2296	0.1451	0.4149	0.1165	0.412	15.3037	44.1411	-2.3466
17	12.9159	19.3866	-7.8046	43.8431	9.3344	29.6742	0.3569	-0.4189	-0.5972	1.5117	-0.1063	-1.813	1.0326	1.0986	-0.2506	0.2908	-0.0046	0.0275	0.3303	0.2127	0.7367	17.8932	49.2267	3.6602
18	9.1966	14.0782	9.156	23.3789	6.2063	23.1316	0.3089	0.1848	-0.2243	0.2794	-0.2454	-0.5096	0.3563	1.5088	-0.0635	0.3247	-0.0345	0.058	0.34	-0.0735	0.4813	17.7064	55.6343	6.4782
19	27.6599	10.0377	17.8494	20.6081	5.8543	17.7954	-0.3005	0.7616	0.6792	-0.095	0.3448	-1.1083	-1.0892	0.8008	-0.0443	0.4163	-0.099	0.0481	0.3301	-0.0244	0.4381	17.8212	62.6801	13.0068
20	5.3004	20.3564	7.9583	67.7963	27.7411	9.1412	-0.6205	0.4422	0.1375	-1.1199	0.6458	0.6331	-0.4448	0.3245	-0.0252	0.8817	-0.1388	-0.1488	0.9077	-0.1097	0.7124	17.8755	71.7875	18.7987

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	45 - 50
2	X-RAY DIFFRACTION	2	A	51 - 59
3	X-RAY DIFFRACTION	3	A	60 - 67
4	X-RAY DIFFRACTION	4	A	68 - 73
5	X-RAY DIFFRACTION	5	A	74 - 79
6	X-RAY DIFFRACTION	6	A	80 - 87
7	X-RAY DIFFRACTION	7	A	88 - 132
8	X-RAY DIFFRACTION	8	A	133 - 137
9	X-RAY DIFFRACTION	9	A	138 - 142
10	X-RAY DIFFRACTION	10	A	143 - 149
11	X-RAY DIFFRACTION	11	A	150 - 154
12	X-RAY DIFFRACTION	12	A	155 - 159
13	X-RAY DIFFRACTION	13	A	160 - 164
14	X-RAY DIFFRACTION	14	A	165 - 168
15	X-RAY DIFFRACTION	15	A	169 - 175
16	X-RAY DIFFRACTION	16	A	176 - 181
17	X-RAY DIFFRACTION	17	A	182 - 186
18	X-RAY DIFFRACTION	18	A	187 - 191
19	X-RAY DIFFRACTION	19	A	192 - 198
20	X-RAY DIFFRACTION	20	A	199 - 204

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