PDB-9nt6: Crystal structure of ecLacI transcription factor ancestor 4 bound...

ID or keywords:

Entry

Database: PDB / ID: 9nt6

Title

Crystal structure of ecLacI transcription factor ancestor 4 bound to Beta-methyl-D-galactoside

Components

LacI Transcription Factor

Keywords

TRANSCRIPTION / Ancestral sequence reconstruction / transcription factor / LacI / BMDG / Beta-methyl-D-galactoside

Function / homology

methyl beta-D-galactopyranoside

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Georgelin, R.L. / Frkic, R.L. / Tan, L. / Kaczmarski, J. / Jackson, C.J.

Funding support

Australia, 2items

Citation

Journal: To Be Published
Title: Crystal structure of ecLacI transcription factor ancestor 4 bound to Beta-methyl-D-galactoside
Authors: Georgelin, R.L. / Frkic, R.L. / Tan, L. / Kaczmarski, J. / Jackson, C.J.

History

Deposition	Mar 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9nt6.cif.gz	233.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9nt6.ent.gz	187.5 KB	Display	PDB format
PDBx/mmJSON format	9nt6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/9nt6 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/9nt6	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LacI Transcription Factor

B: LacI Transcription Factor

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	36.467, 108.336, 119.601
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

LacI Transcription Factor

Mass: 30166.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Production host:

Escherichia coli (E. coli)

#2: Sugar

ChemComp-MBG / methyl beta-D-galactopyranoside / METHYL-BETA-GALACTOSE / methyl beta-D-galactoside / methyl D-galactoside / methyl galactoside

Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₄O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 21 % PEG 3350, 0.1M HEPES pH 7.1

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.5→49.34 Å / Num. obs: 76948 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.041 / R_rim(I) all: 0.146 / Χ²: 0.82 / Net I/σ(I): 10.8 / Num. measured all: 986424
Reflection shell	Resolution: 1.5→1.53 Å / % possible obs: 98.3 % / Redundancy: 11 % / R_merge(I) obs: 1.767 / Num. measured all: 40988 / Num. unique obs: 3714 / CC_1/2: 0.653 / R_pim(I) all: 0.552 / R_rim(I) all: 1.853 / Χ²: 0.57 / Net I/σ(I) obs: 1.4

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→49.34 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2078	3845	5.01 %
R_work	0.1756	-	-
obs	0.1772	76788	99.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→49.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4114	0	42	409	4565

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.988
X-RAY DIFFRACTION	f_dihedral_angle_d	6.352	619
X-RAY DIFFRACTION	f_chiral_restr	0.059	738
X-RAY DIFFRACTION	f_plane_restr	0.01	799

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 (%)
1.5-1.52	0.2804	131	0.2415	2633	X-RAY DIFFRACTION	98
1.52-1.54	0.2582	137	0.2324	2629	X-RAY DIFFRACTION	100
1.54-1.56	0.2311	158	0.2295	2639	X-RAY DIFFRACTION	100
1.56-1.58	0.2784	156	0.2204	2688	X-RAY DIFFRACTION	100
1.58-1.61	0.2171	143	0.2183	2629	X-RAY DIFFRACTION	100
1.61-1.63	0.2557	141	0.2096	2662	X-RAY DIFFRACTION	100
1.63-1.66	0.2391	142	0.2039	2691	X-RAY DIFFRACTION	99
1.66-1.69	0.2969	124	0.2349	2665	X-RAY DIFFRACTION	100
1.69-1.72	0.2584	148	0.2313	2662	X-RAY DIFFRACTION	100
1.72-1.75	0.2685	138	0.2215	2673	X-RAY DIFFRACTION	100
1.75-1.79	0.2252	147	0.2112	2671	X-RAY DIFFRACTION	100
1.79-1.82	0.2585	147	0.195	2686	X-RAY DIFFRACTION	100
1.82-1.87	0.2328	146	0.1889	2666	X-RAY DIFFRACTION	100
1.87-1.91	0.2194	130	0.1815	2690	X-RAY DIFFRACTION	100
1.91-1.97	0.2097	130	0.1786	2687	X-RAY DIFFRACTION	100
1.97-2.02	0.2204	153	0.1799	2713	X-RAY DIFFRACTION	100
2.02-2.09	0.2337	147	0.1902	2657	X-RAY DIFFRACTION	100
2.09-2.16	0.2112	134	0.1844	2728	X-RAY DIFFRACTION	100
2.16-2.25	0.2001	171	0.1715	2657	X-RAY DIFFRACTION	100
2.25-2.35	0.2089	128	0.169	2715	X-RAY DIFFRACTION	100
2.35-2.48	0.2047	153	0.1734	2724	X-RAY DIFFRACTION	100
2.48-2.63	0.2145	145	0.1759	2722	X-RAY DIFFRACTION	100
2.63-2.83	0.1901	126	0.178	2752	X-RAY DIFFRACTION	100
2.83-3.12	0.2312	139	0.1733	2762	X-RAY DIFFRACTION	100
3.12-3.57	0.1957	134	0.1601	2776	X-RAY DIFFRACTION	100
3.57-4.5	0.1738	143	0.1374	2816	X-RAY DIFFRACTION	100
4.5-49.34	0.1486	154	0.1528	2950	X-RAY DIFFRACTION	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	3.3257	-0.6897	-2.5292	2.075	1.2424	7.5557	0.0121	-0.016	0.0697	-0.0623	-0.0453	-0.1568	0.01	0.2686	0.0223	0.1124	-0.0087	-0.0142	0.0601	0.0175	0.1229	26.7114	-8.902	-31.4298
2	1.2306	-0.267	-0.6571	2.1232	-1.7829	3.1938	0.0528	0.1554	-0.0441	-0.1894	0.0375	0.2214	0.33	-0.2534	-0.0902	0.2028	-0.0178	-0.0411	0.1825	-0.0457	0.1828	17.125	-15.3706	-36.1905
3	2.4579	-0.6138	1.1016	3.1862	-1.4947	5.4496	-0.0695	-0.0366	-0.2113	-0.0158	0.0636	0.0136	0.1843	-0.0639	0.0113	0.0735	-0.0348	0.0118	0.0446	0.0018	0.1225	14.4509	-20.5907	-7.2238
4	2.045	0.219	-0.5439	5.7747	-4.8944	8.7663	-0.0249	0.2214	-0.1757	-0.4965	0.2025	0.3048	0.4599	-0.444	-0.1885	0.1332	-0.0389	0.0027	0.1496	-0.0271	0.1792	10.4729	-23.5896	-13.5251
5	1.0491	-0.134	0.2821	1.0485	-0.18	1.0512	-0.0404	-0.0778	0.0081	0.0635	0.0671	0.1203	-0.0198	-0.1071	-0.0268	0.0807	0.0129	0.007	0.097	0.0039	0.1073	12.4258	-9.4843	-5.8748
6	0.475	-0.8802	-1.9073	2.6374	3.4585	7.8903	-0.019	0.0279	-0.0118	-0.2005	-0.0071	-0.0235	-0.007	0.1762	-0.0141	0.0865	0.0175	-0.0072	0.1302	0.003	0.1031	28.0524	-15.6642	-23.9747
7	1.0487	-0.3033	-0.5376	1.5759	1.7025	6.6135	-0.0112	0.1942	-0.1346	-0.0034	-0.0229	0.0078	0.5535	-0.2308	0.0858	0.149	-0.0061	0.0041	0.1287	-0.0082	0.1344	24.098	-20.7724	-14.522
8	2.7096	0.3781	-0.3131	3.2924	0.7992	6.5938	0.2169	0.2577	-0.0532	-0.2735	-0.0784	0.0117	-0.3282	-0.2693	-0.1002	0.1655	0.0466	-0.0109	0.1145	-0.0096	0.1547	20.0079	3.0671	-34.1945
9	2.4042	2.2478	-0.4853	3.5868	-0.5635	3.6756	0.2498	0.4081	-0.2153	-0.535	0.3307	-1.4649	-0.8788	0.623	-0.3113	0.5204	-0.0534	0.2649	0.3392	-0.0945	0.6941	29.756	8.9452	-41.2524
10	0.4825	0.6332	1.7085	2.0769	1.5881	6.1003	-0.1011	0.1628	0.0133	-0.5781	0.1894	-0.2764	-0.4879	0.3484	-0.1059	0.2907	-0.0428	0.029	0.1667	0.0155	0.2567	25.2823	20.5994	-21.046
11	1.0077	0.1996	0.1684	1.8464	0.3931	0.8652	-0.0539	0.0104	0.0186	-0.0348	0.0865	-0.1436	-0.0559	0.1088	-0.0236	0.1112	0.0011	-0.0073	0.119	-0.0116	0.1357	31.2438	12.3001	-8.6026
12	1.3305	-0.6728	0.5528	1.5633	0.3217	4.6121	0.0964	0.2511	0.0653	-0.3608	-0.1414	0.0642	-0.4032	0.0093	0.0593	0.178	0.0351	-0.0211	0.1374	0.01	0.1566	18.1135	15.351	-19.951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 61 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 162 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 163 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 206 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 207 through 278 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 279 through 306 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 307 through 331 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 59 through 102 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 103 through 146 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 147 through 175 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 176 through 278 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 279 through 335 )

-
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