PDB-2f7b: CatM effector binding domain

Basic information

• Entry: Database: PDB / ID: 2f7b
• Title: CatM effector binding domain
• Components: HTH-type transcriptional regulator catM
• Keywords: GENE REGULATION / LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain

Function / homology

Function:

catabolic process / protein-DNA complex / DNA-binding transcription factor activity / DNA binding

Domain/homology:

: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta

Component:

HTH-type transcriptional regulator CatM

• Biological species: Acinetobacter baylyi (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.

#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of the effector-binding domains of BenM and CatM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1.
Authors: Clark, T. / Haddad, S. / Neidle, E. / 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 / Derived calculations / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _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 / Derived calculations / Refinement description Category: 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: HTH-type transcriptional regulator catM

hetero molecules

Summary:

• 26.6 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	26,632	6
Polymers	26,213	1
Non-polymers	420	5
Water	6,467	359

1

A: HTH-type transcriptional regulator catM

hetero molecules

A: HTH-type transcriptional regulator catM

hetero molecules

Summary:

• defined by author&software
• 53.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	53,265	12
Polymers	52,425	2
Non-polymers	839	10
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_756	-x+2,y,-z+1	1

Calculated values:

Buried area	4170 Å2
ΔGint	-134 kcal/mol
Surface area	18790 Å2
Method	PISA

2

A: HTH-type transcriptional regulator catM

hetero molecules

A: HTH-type transcriptional regulator catM

hetero molecules

A: HTH-type transcriptional regulator catM

hetero molecules

A: HTH-type transcriptional regulator catM

hetero molecules

Summary:

• defined by software
• 107 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	106,529	24
Polymers	104,851	4
Non-polymers	1,679	20
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_755	-x+2,-y,z	1
crystal symmetry operation	3_756	-x+2,y,-z+1	1
crystal symmetry operation	4_556	x,-y,-z+1	1

Calculated values:

Buried area	11770 Å2
ΔGint	-358 kcal/mol
Surface area	34910 Å2
Method	PISA, PQS

Unit cell

Length a, b, c (Å)	66.184, 75.529, 102.189
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-1004- SO4

• 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

Components

#1: Protein

A HTH-type transcriptional regulator catM / Cat operon transcriptional regulator

Details:

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

A-1001 A-1002 A-1003 A-1004
ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄

#3: Chemical

A-1005 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.6 ų/Da / Density % sol: 52.4 %
• 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: 1.00727 Å
• Detector: Type: MARRESEARCH / Detector: CCD
• Radiation: Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.00727 Å / Relative weight: 1
• Reflection: Resolution: 1.8→60.746 Å / Num. all: 22581 / Num. obs: 22581 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / B_iso Wilson estimate: 20.47029 Ų / R_merge(I) obs: 0.056 / Net I/σ(I): 29.7
• Reflection shell: Resolution: 1.8→1.86 Å / % possible obs: 88.7 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 7.5 / Num. measured obs: 2107 / Num. unique all: 2107 / Χ²: 1.44 / % possible all: 88.7

Processing

Software

Name	Version	Classification	NB
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 2F6G

2f6g

Resolution: 1.9→60.746 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.914 / WR_factor R_free: 0.257 / WR_factor R_work: 0.186 / SU B: 7.879 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: 14 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.159 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2399	1007	5.186 %	Random
Rwork	0.1718	-	-	-
all	0.175	18410	-	-
obs	0.175	18410	94.441 %	-

• 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: 19.847 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.296 Å2	0 Å2	0 Å2
2-	-	0.682 Å2	0 Å2
3-	-	-	-0.978 Å2

Refinement step

Cycle: LAST / Resolution: 1.9→60.746 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1688	0	21	359	2068

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1754
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1781
X-RAY DIFFRACTION	r_angle_refined_deg	1.08	1.994	2387
X-RAY DIFFRACTION	r_angle_other_deg	0.727	3.001	4067
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.391	5	217
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.543	24.521	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.191	15	314
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	16.097	15	3
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.931	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	279
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1925
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	375
X-RAY DIFFRACTION	r_nbd_refined	0.183	0.2	311
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	1862
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	801
X-RAY DIFFRACTION	r_nbtor_other	0.077	0.2	1074
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.124	0.2	253
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.149	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.215	0.2	102
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.078	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.778	2	1403
X-RAY DIFFRACTION	r_mcbond_other	0.081	2	432
X-RAY DIFFRACTION	r_mcangle_it	1.17	5	1755
X-RAY DIFFRACTION	r_mcangle_other	0.499	5	1468
X-RAY DIFFRACTION	r_scbond_it	2.362	7	755
X-RAY DIFFRACTION	r_scbond_other	0.74	7	1538
X-RAY DIFFRACTION	r_scangle_it	3.161	10	630
X-RAY DIFFRACTION	r_scangle_other	1.312	10	2599

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Rfactor all	Num. reflection all	% reflection obs (%)
1.9-1.949	0.278	63	0.209	1371	0.212	1471	97.485
1.949-2.003	0.233	79	0.192	1359	0.195	1473	97.624
2.003-2.061	0.254	69	0.186	1310	0.189	1411	97.732
2.061-2.124	0.293	74	0.178	1267	0.184	1377	97.386
2.124-2.194	0.496	38	0.354	501	0.365	1349	39.956
2.194-2.27	0.263	57	0.178	1214	0.182	1299	97.844
2.27-2.356	0.195	60	0.18	1163	0.181	1249	97.918
2.356-2.452	0.215	70	0.176	1139	0.178	1228	98.453
2.452-2.561	0.225	50	0.175	1093	0.177	1157	98.79
2.561-2.686	0.215	66	0.169	1021	0.172	1102	98.639
2.686-2.831	0.258	50	0.179	996	0.182	1060	98.679
2.831-3.002	0.249	53	0.167	957	0.171	1018	99.214
3.002-3.209	0.179	52	0.162	869	0.162	932	98.82
3.209-3.465	0.211	49	0.151	842	0.154	900	99
3.465-3.794	0.224	49	0.146	764	0.15	819	99.267
3.794-4.24	0.257	35	0.139	708	0.144	746	99.598
4.24-4.892	0.204	29	0.129	626	0.132	659	99.393
4.892-5.982	0.214	25	0.167	549	0.169	576	99.653
5.982-8.419	0.206	22	0.189	431	0.19	457	99.125
8.419-60.746	0.318	17	0.247	230	0.251	277	89.17

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	2.9727	-0.4633	-0.1863	3.0786	1.4061	2.868	-0.0611	0.0458	-0.0361	-0.0047	-0.0038	0.1243	-0.1851	-0.0989	0.065	-0.0416	0.0031	0.017	0.034	0.0244	-0.0484	50.796	17.883	55.696
2	7.2183	3.4069	-2.0658	17.3811	-4.4733	8.6557	-0.4214	0.3347	0.3727	-1.0185	0.411	0.2282	-0.2376	0.0304	0.0105	-0.0773	-0.0002	-0.0596	0.2067	0.019	0.0756	40.09	17.199	50.73
3	4.8257	-0.2011	-1.2802	1.4605	0.7196	1.9671	-0.0287	-0.0161	0.4274	0.0606	0.0315	-0.0434	-0.3242	0.002	-0.0028	0.0119	0.0132	0.0073	-0.0354	0.0225	-0.0153	52.96	27.644	61.733
4	11.8036	4.4321	8.0417	5.554	1.457	8.6977	-0.212	-0.2231	-0.03	0.3762	0.0608	-0.2257	-0.4974	0.2675	0.1512	0.0206	0.0083	0.0458	0.0204	-0.0098	-0.0256	50.894	27.065	72.291
5	16.9209	-10.5499	-6.7254	6.7683	4.8121	4.6831	-0.3005	-0.2932	-0.1059	0.3319	0.2356	-0.2159	-0.2842	0.125	0.0649	0.0023	-0.0042	0.036	0.0153	0.0345	0.0102	55.57	13.487	69.363
6	5.9591	-1.2712	-2.9261	4.9741	0.7056	3.8041	0.1611	-0.1486	-0.0547	0.0651	0.1045	-0.4852	0.0982	0.294	-0.2656	-0.0355	0.0118	-0.0674	0.0158	-0.0177	0.0011	78.937	7.773	62.274
7	3.0921	2.8266	0.7595	14.7512	5.8754	2.9319	-0.1213	0.0659	-0.0309	0.0715	0.1679	-0.302	0.0154	0.3875	-0.0466	-0.0097	-0.0081	-0.0687	0.007	-0.0122	-0.028	78.9	8.982	71.497
8	17.0563	-5.7403	1.5052	7.2752	-1.7669	2.357	-0.268	-0.0877	0.0141	0.4952	0.0736	-0.1626	-0.3994	0.0673	0.1944	0.0091	-0.0708	-0.0281	0.0077	0.0003	-0.0803	74.582	23.065	63.186
9	4.6898	-1.9969	2.6958	1.0235	-2.072	6.4807	-0.1678	-0.2909	0.2801	0.1978	0.0181	-0.0855	-0.5668	-0.0237	0.1497	0.0291	-0.031	-0.0617	0.0134	-0.046	0.0226	72.837	22.843	71.58
10	1.3895	0.3878	1.2399	5.2489	-0.1664	1.1574	0.0204	0.057	0.1087	-0.1198	-0.0458	-0.0946	-0.2101	0.0791	0.0254	0.0012	-0.0177	0.0033	0.0514	-0.0016	-0.0253	74.156	20.411	56.481
11	6.5227	2.9629	2.2072	3.194	0.5818	2.7306	-0.0905	0.0864	0.1025	-0.1527	0.1465	0.0135	0.1311	0.104	-0.056	-0.0076	0.0002	0.0011	0.0289	0.0171	0.0031	70.619	12.896	60.437
12	0.4466	-0.0589	-1.6397	1.0612	0.4062	8.6489	-0.1062	-0.0096	-0.0217	0.1431	-0.1361	-0.0008	0.2055	-0.2822	0.2422	-0.0378	-0.024	-0.0013	0.0331	-0.025	-0.001	71.787	8.934	64.237
13	2.1528	-1.5742	1.8265	4.4081	-0.0256	2.0766	-0.1283	-0.3363	-0.1773	0.2095	-0.0664	0.3179	-0.159	-0.3051	0.1947	-0.0553	0.0443	0.0705	0.0849	0.0164	-0.0147	44.194	20.837	64.908
14	6.2677	-0.7168	4.8656	3.8434	-1.564	4.047	0.0627	-0.2817	0.1996	0.4102	-0.0251	0.4071	-0.1308	-0.4761	-0.0375	-0.0193	-0.0056	0.0586	0.0263	0.0156	0.0481	48.838	6.237	65.78

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	90 - 112	10 - 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 - 303	210 - 223