PDB-2f7c: CatM effector binding domain with its effector cis,cis-muconate

ID or keywords:

Entry

Database: PDB / ID: 2f7c

Title

CatM effector binding domain with its effector cis,cis-muconate

Components

HTH-type transcriptional regulator catM

Keywords

GENE REGULATION /

LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain /

muconate

Function / homology

Function and homology information

: / DNA-binding transcription factor activity /

Biological species

Acinetobacter baylyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.162 Å

Authors

Clark, T. / Haddad, S. / Ezezika, O. / Neidle, E. / Momany, C.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator.
Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C.

History

Deposition	Nov 30, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Aug 23, 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

-
Download

PDBx/mmCIF format	2f7c.cif.gz	64 KB	Display	PDBx/mmCIF format
PDB format	pdb2f7c.ent.gz	46.2 KB	Display	PDB format
PDBx/mmJSON format	2f7c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/2f7c ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f7c	HTTPS FTP

-
Related structure data

Related structure data	2f6gC 2f6pC 2f78C 2f7aC 2f7bSC 2f8d 2f97 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2h98-d 3d0s-d 2f7b-1 4ra1-d 4mp2-d 5osi-3 3zdp-1 3q1g-1 6hfb-1 6fmo-4 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HTH-type transcriptional regulator catM

hetero molecules

26.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HTH-type transcriptional regulator catM

hetero molecules

A: HTH-type transcriptional regulator catM

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.568, 73.108, 102.627
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-428- HOH

Details

The biological unit (effector binding domain) is a dimer generated from the monomer in the asymmetric unit by the operation, 1-x, y, -z

#1: Protein	HTH-type transcriptional regulator catM / Cat operon transcriptional regulator Mass: 26212.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: catM, catR / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07774
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CCU / (2Z,4Z)-HEXA-2,4-DIENEDIOIC ACID / CIS,CIS-MUCONIC ACID / Muconic acid Mass: 142.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₆O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.54 %
Crystal grow	Temperature: 288 K / Method: microbatch under oil Details: PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.16→59.549 Å / Num. all: 13349 / Num. obs: 13349 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / B_iso Wilson estimate: 44.08847 Å² / R_merge(I) obs: 0.079 / Net I/σ(I): 42.8
Reflection shell	Resolution: 2.17→2.25 Å / % possible obs: 82.1 % / Redundancy: 4.3 % / R_merge(I) obs: 0.537 / Mean I/σ(I) obs: 4.1 / Num. measured obs: 1099 / Num. unique all: 1099 / R_sym value: 0.537 / Χ²: 3.09 / % possible all: 82.1

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 2F7B

2f7b

Resolution: 2.162→59.549 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.922 / WR_factor R_free: 0.236 / WR_factor R_work: 0.182 / SU B: 11.986 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement with 14 groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.21 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	657	4.952 %	Random
R_work	0.1823	-	-	-
all	0.185	12611	-	-
obs	0.185	12611	97.991 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 38.375 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.597 Å²	0 Å²	0 Å²
2-	-	1.703 Å²	0 Å²
3-	-	-	-1.106 Å²

Refinement step

Cycle: LAST / Resolution: 2.162→59.549 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1700	0	15	202	1917

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1761
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1795
X-RAY DIFFRACTION	r_angle_refined_deg	1.159	1.996	2390
X-RAY DIFFRACTION	r_angle_other_deg	0.751	3.005	4091
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.663	5	215
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.658	24.324	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.13	15	315
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	16.934	15	3
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.112	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	281
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1949
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	385
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	339
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	1887
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	832
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	1076
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	154
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.249	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.221	0.2	104
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.147	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.845	2	1413
X-RAY DIFFRACTION	r_mcbond_other	0.089	2	436
X-RAY DIFFRACTION	r_mcangle_it	1.281	5	1765
X-RAY DIFFRACTION	r_mcangle_other	0.551	5	1476
X-RAY DIFFRACTION	r_scbond_it	2.65	7	759
X-RAY DIFFRACTION	r_scbond_other	0.907	7	1552
X-RAY DIFFRACTION	r_scangle_it	3.447	10	625
X-RAY DIFFRACTION	r_scangle_other	1.365	10	2615

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	R_factor all	Num. reflection all	% reflection obs (%)
2.162-2.218	0.297	44	0.227	809	0.231	980	87.041
2.218-2.279	0.327	50	0.235	860	0.24	947	96.093
2.279-2.345	0.293	50	0.221	877	0.225	949	97.682
2.345-2.417	0.354	27	0.233	843	0.237	884	98.416
2.417-2.496	0.316	47	0.212	818	0.217	876	98.744
2.496-2.583	0.354	44	0.213	806	0.22	861	98.722
2.583-2.681	0.257	45	0.195	769	0.199	820	99.268
2.681-2.79	0.206	45	0.191	755	0.192	805	99.379
2.79-2.914	0.24	31	0.201	730	0.203	764	99.607
2.914-3.056	0.258	43	0.196	687	0.2	733	99.591
3.056-3.22	0.227	36	0.184	659	0.186	699	99.428
3.22-3.415	0.206	27	0.176	629	0.177	656	100
3.415-3.65	0.237	41	0.177	589	0.181	631	99.842
3.65-3.941	0.24	22	0.157	566	0.16	588	100
3.941-4.316	0.232	27	0.16	512	0.164	539	100
4.316-4.822	0.227	16	0.135	475	0.138	492	99.797
4.822-5.562	0.124	13	0.159	432	0.158	446	99.776
5.562-6.797	0.237	22	0.203	346	0.205	372	98.925
6.797-9.55	0.2	20	0.163	281	0.165	304	99.013
9.55-59.549	0.291	7	0.234	168	0.236	194	90.206

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	7.1307	1.5183	1.0914	3.548	2.1877	2.0991	-0.0871	0.2248	-0.0036	-0.1487	-0.0414	0.1176	-0.1368	0.0141	0.1286	-0.0628	0.0017	0.01	0.0402	0.0065	-0.176	50.218	18.026	55.472
2	9.8492	5.6871	5.7674	25.4231	3.2004	13.8922	-0.3429	0.894	0.1316	-0.9596	-0.1474	0.4665	-0.5486	0.3688	0.4903	-0.245	0.0048	-0.1291	0.2143	-0.0257	0.0093	40.125	17.413	50.297
3	4.5132	0.3306	-1.4184	5.9942	0.183	2.0939	-0.0508	-0.2895	0.676	-0.2245	-0.0759	0.0028	-0.2657	0.0426	0.1267	-0.072	0.0248	-0.0354	-0.0572	-0.0437	-0.0697	52.675	27.219	62.14
4	5.1107	0.9244	-0.1666	8.9593	5.3735	9.0554	-0.1121	-1.2207	0.2614	0.4751	-0.2142	-0.0562	-0.4168	0.3903	0.3263	-0.0957	-0.0348	0.0245	0.2015	-0.1153	-0.1019	50.169	27.051	72.377
5	30.8723	-3.8275	-8.979	5.5788	0.2483	8.7319	-0.0514	-1.4821	-1.3956	0.1079	0.1431	0.1481	0.284	-0.151	-0.0917	-0.061	-0.0273	0.0272	0.0308	-0.0646	-0.1469	54.903	12.567	69.379
6	10.0492	-1.1624	-4.2153	6.229	2.292	6.0422	0.0214	0.0044	-0.2164	0.0141	0.063	-0.4046	-0.0455	0.1506	-0.0844	-0.1044	-0.0091	-0.0429	0.0047	0.0181	-0.1109	78.325	7.172	62.676
7	3.4086	1.5896	-1.0496	11.897	6.1817	4.3125	-0.0569	-0.6932	-0.0888	0.2676	0.0466	-0.4676	0.1545	0.3621	0.0103	-0.0482	-0.0302	-0.0759	0.1018	0.0183	-0.096	78.222	8.045	71.834
8	10.2181	-3.8498	-0.8882	3.8908	-0.782	1.9205	0.1259	-0.4042	0.148	-0.2743	-0.0301	-0.1501	-0.0647	0.0874	-0.0957	-0.0305	-0.0367	0.0019	0.0086	-0.0241	-0.1435	73.406	22.272	63.984
9	5.4784	-2.3582	5.6548	1.3571	-2.3248	5.872	-0.1752	-0.4293	0.3781	0.1131	0.1069	-0.0689	-0.3382	-0.1041	0.0683	-0.0684	-0.0301	-0.005	0.1276	-0.1007	-0.0781	71.911	21.7	72.271
10	0.8365	0.0137	-1.9928	3.0635	0.8724	5.0149	0.0273	0.0966	0.2897	-0.3298	-0.0326	-0.1521	-0.3501	0.1004	0.0053	0.0106	0.0276	0.0041	0.0643	0.0055	-0.104	73.356	19.965	57.293
11	19.4844	5.7705	-1.8791	5.5924	3.6878	4.8199	-0.0226	0.1541	0.0408	-0.2361	-0.0015	-0.0478	-0.0953	-0.1635	0.0242	-0.0221	0.0458	-0.0152	0.0076	0.0825	-0.1314	69.845	12.309	60.818
12	1.7858	0.4183	-2.1305	2.8423	-2.3053	5.8343	-0.055	-0.0168	-0.0483	0.1981	-0.1485	-0.0738	0.4406	-0.4222	0.2035	-0.0857	-0.0575	-0.0111	0.0959	-0.0222	-0.139	71.129	8.033	64.59
13	2.1937	-1.4275	2.5069	3.7071	-0.1554	3.8195	-0.0729	-0.4267	0.0731	0.01	-0.0787	0.2874	-0.2828	-0.4325	0.1516	-0.1233	0.0425	0.0718	0.1021	-0.0224	-0.0862	43.858	20.769	64.828
14	4.2206	-0.9941	2.1213	14.9131	-1.6159	1.151	-0.1035	-0.2633	-0.0168	0.8898	0.0711	1.2481	0.1383	-0.4376	0.0324	0.0039	-0.0106	0.1305	0.0555	-0.0422	-0.0547	47.614	6.491	65.977

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	89 - 112	9 - 32
2	2	113 - 120	33 - 40
3	3	121 - 148	41 - 68
4	4	149 - 156	69 - 76
5	5	157 - 163	77 - 83
6	6	164 - 175	84 - 95
7	7	176 - 188	96 - 108
8	8	189 - 199	109 - 119
9	9	200 - 220	120 - 140
10	10	221 - 237	141 - 157
11	11	238 - 250	158 - 170
12	12	251 - 266	171 - 186
13	13	267 - 289	187 - 209
14	14	290 - 304	210 - 224

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi