PDB-9nlm: GloR with selenomethionine labels

ID or keywords:

Entry

Database: PDB / ID: 9nlm

Title

GloR with selenomethionine labels

Components

LysR family transcriptional regulator

Keywords

CYTOSOLIC PROTEIN / glyoxal

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Cuthbert, B.J. / de Miranda, R. / Martinez, J. / Goulding, C.W.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: A glyoxal-specific transcription factor
Authors: Corcoran, C.P. / Cuthbert, B.J. / Glanville, D.G. / de Miranda, R. / Martinez, J. / Goulding, C.W. / Ulijasz, A.T.

History

Deposition	Mar 3, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nlm.cif.gz	380.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9nlm.ent.gz	262.6 KB	Display	PDB format
PDBx/mmJSON format	9nlm.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/nl/9nlm ftp://data.pdbj.org/pub/pdb/validation_reports/nl/9nlm	HTTPS FTP

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Related structure data

Related structure data	9nliC 9nrqC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LysR family transcriptional regulator

B: LysR family transcriptional regulator

C: LysR family transcriptional regulator

D: LysR family transcriptional regulator

hetero molecules

90.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LysR family transcriptional regulator

C: LysR family transcriptional regulator

hetero molecules

defined by author&software
Evidence: gel filtration
45.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LysR family transcriptional regulator

D: LysR family transcriptional regulator

hetero molecules

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

Unit cell

Length a, b, c (Å)	149.078, 149.078, 75.813
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁
Space group name Hall	P6₁
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: -x,-y,z+1/2

#1: Protein	LysR family transcriptional regulator Mass: 22386.352 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: DT376_05080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A367MEI0
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.72 Å³/Da / Density % sol: 54.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4 % Tacsimate pH 7.0, 12 % PEG3350 / Temp details: room temperature

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.97961, 0.97944, 0.91161

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2023

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97961	1
2	0.97944	1
3	0.91161	1

Reflection

Entry-ID: 9NLM / Diffraction-ID: 1

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	R_rim(I) all	Χ²	Net I/σ(I)
2.5-37.43	25341	99.5	12.9	0.999	0.078	0.033	0.085	1.03	16
2.49-37.43	33443	99	17.4	0.994	0.202	0.069	0.214	17.4	9.7
2.49-37.44	588602	99.4	17.5	0.997	0.168	0.057	0.177	0.95	10.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.5-2.6	11.7	1.239	2.1	1726	0.827	0.54	1.356	1.04	97.6
2.5-2.59	15.7	4.063	2	3504	0.79	1.498	4.343	0.92	92.4
2.5-2.59	17.2	3.32	1.7	3635	0.527	1.157	3.522	1.04	96

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 2.5→37.43 Å / SU ML: 0.4055 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.2517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2521	3358	10.06 %
R_work	0.2143	30009	-
obs	0.2181	33367	99.49 %

Solvent computation

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

Displacement parameters

B_iso mean: 92.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→37.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5942	0	30	8	5980

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0099	6158
X-RAY DIFFRACTION	f_angle_d	1.1494	8400
X-RAY DIFFRACTION	f_chiral_restr	0.0589	947
X-RAY DIFFRACTION	f_plane_restr	0.011	1115
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9736	2209

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 (%)
2.5-2.53	0.4007	129	0.3651	1172	X-RAY DIFFRACTION	93.4
2.53-2.57	0.3911	137	0.3323	1230	X-RAY DIFFRACTION	99.93
2.57-2.61	0.4023	140	0.3314	1257	X-RAY DIFFRACTION	99.93
2.61-2.65	0.4251	138	0.3128	1238	X-RAY DIFFRACTION	100
2.65-2.7	0.3878	143	0.2945	1265	X-RAY DIFFRACTION	99.79
2.7-2.75	0.3126	139	0.2823	1241	X-RAY DIFFRACTION	100
2.75-2.8	0.3522	136	0.285	1256	X-RAY DIFFRACTION	100
2.8-2.86	0.3625	139	0.2929	1216	X-RAY DIFFRACTION	99.85
2.86-2.92	0.3725	143	0.2715	1263	X-RAY DIFFRACTION	99.43
2.92-2.99	0.3395	141	0.2797	1254	X-RAY DIFFRACTION	99.64
2.99-3.06	0.3427	138	0.2783	1230	X-RAY DIFFRACTION	99.85
3.06-3.14	0.3179	140	0.254	1247	X-RAY DIFFRACTION	100
3.14-3.24	0.3236	140	0.2478	1268	X-RAY DIFFRACTION	99.79
3.24-3.34	0.2831	133	0.2425	1225	X-RAY DIFFRACTION	97.49
3.34-3.46	0.2906	140	0.2253	1251	X-RAY DIFFRACTION	100
3.46-3.6	0.3017	141	0.2299	1254	X-RAY DIFFRACTION	99.93
3.6-3.76	0.2773	139	0.2039	1249	X-RAY DIFFRACTION	99.93
3.76-3.96	0.2541	142	0.2069	1262	X-RAY DIFFRACTION	100
3.96-4.21	0.2385	141	0.1943	1264	X-RAY DIFFRACTION	99.86
4.21-4.53	0.1888	142	0.1778	1268	X-RAY DIFFRACTION	100
4.53-4.99	0.1928	140	0.1667	1254	X-RAY DIFFRACTION	99.86
4.99-5.71	0.2241	146	0.1983	1260	X-RAY DIFFRACTION	99.93
5.71-7.18	0.2399	143	0.2262	1285	X-RAY DIFFRACTION	99.86
7.2-37.43	0.1793	148	0.1762	1300	X-RAY DIFFRACTION	99.38

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	7.70674284958	0.443504217359	0.750500545196	4.45251969283	-0.902984583973	4.10078934233	-0.459042894848	2.25238334637	0.197797892581	-1.33612841061	0.440361083246	0.419605731178	0.254755294527	0.176089966527	-0.0663110388242	0.810478530585	-0.115476274828	-0.16433172078	0.975696922589	0.0503351148423	0.535419123198	77.4990979715	84.0054570112	-5.45119717916
2	6.82797965002	0.85707775157	-0.560048231186	2.82132490128	-0.248054246648	5.74686495317	-0.410648131292	1.73156811056	1.60364807127	-1.20822314644	0.0802564373759	0.69047070483	-0.780715905786	0.0414782374948	0.408297557243	0.76019276505	-0.0715841080622	-0.208766954499	0.862108872632	0.222905156565	0.743650291942	75.1017628121	91.5562065112	-0.223193268634
3	3.41697848617	-3.27044329714	1.03628590173	9.21653768483	5.07088454294	6.55374327279	0.243122095309	0.0656535468942	0.35149844864	-0.259257729393	-0.55488696897	2.21739486533	0.59235025612	-0.841578818631	0.010095310497	0.509779411227	-0.042205448304	-0.170588519526	0.618078948457	0.169930134361	1.11439091576	50.6934010248	79.4907567697	12.3190998179
4	3.46452696516	-1.64199380465	2.62675910716	7.9444321965	1.92305603311	3.25592975093	0.0368959585519	0.440747456152	0.557009533819	-0.79503195888	-0.197737247468	-0.0796999418376	-0.226968808489	-0.338685723616	-0.0340555529178	0.567936095899	0.0209215535727	0.142438276803	0.852054151071	0.28710324364	0.891661201571	52.3586045469	46.6733963202	13.2939711304
5	3.36537532859	2.4211411782	3.06880097997	7.90772941534	-2.86663158636	6.70311644565	-0.220777282447	0.280271869001	0.490286809531	-1.28961582513	-0.717080032986	0.78772857471	0.207590014449	0.558096382649	1.22027887419	0.902103311028	0.0213918530808	-0.109643221985	1.22755202607	0.292143418708	0.91065184658	47.2195491992	57.0271190569	8.69526072491
6	0.726670846508	0.273736586399	0.76114386442	3.95653580641	-0.185589436813	5.87031306183	0.605882540298	0.166730574252	1.22369940694	0.642465819221	-0.0913250330881	1.60034170161	-0.844055655482	-1.08163722524	-0.47900941859	1.04858660718	0.0476292223715	0.630974265627	0.937085194342	0.112323238292	1.64436107789	42.5651219659	57.7349291117	29.5074039707
7	5.57239121286	-0.923328432687	1.3500571698	1.74705203157	-1.10470522444	0.818071557765	0.0438857730045	0.117748552006	2.0252810236	-0.11808767927	-0.513996621862	0.302338623652	-0.412284735199	-0.287365950707	0.326630264081	1.40723900852	0.00270981710851	0.513920974143	0.777080150729	0.132262848783	1.90414032761	49.2695035554	67.4056662343	31.5994894919
8	0.475472152834	-0.61908997274	0.828972116009	6.81564299697	-0.986917426068	1.8783574482	0.57339405167	-0.655240142857	2.2982134995	0.71492850495	-0.164484436475	0.474703899882	-1.44316734979	-0.164494735641	-0.321225129196	0.994846798655	-0.093833873308	0.500326579275	0.66670764806	-0.2651260984	1.55763727688	52.9663004976	60.4137047932	36.0126314839
9	5.75243767888	0.399489066839	-1.27938588429	2.12844919312	-1.57301831311	7.18711205657	0.561428434833	-0.51726541875	1.27721413878	0.404412632953	0.0350922955256	-0.028419347204	-1.22664955954	-0.352479664345	-0.605771226915	0.932811783006	-0.139655109825	0.330356241188	0.597492863297	-0.231538660236	1.30638706218	45.0951167675	55.6217880061	37.2519089745
10	6.6144834787	-1.43576423193	1.53825286015	2.12825607109	1.7937906372	5.0475898194	0.507325368662	0.841122792546	-0.471929197633	-2.03363442272	-0.333054677106	1.4485586254	-0.356529191417	-0.90895658877	0.134602727755	1.03956122843	-0.0390487710394	-0.110848342854	1.08634568882	0.156897238519	0.878254224052	44.1240376022	48.2968854211	8.34920003925
11	7.03921331242	-0.27818688452	0.390546670065	8.83392241809	-1.91003901951	7.45495031014	-0.0485977806783	0.324131704649	-0.109923473017	-0.31497266006	0.11598032769	-0.00261709076701	0.300832957168	-0.288858396373	-0.0848281225828	0.303974079045	-0.0372349753756	-0.11747105785	0.459094557209	-0.0200857139579	0.475644501417	87.0052997527	78.9895097807	11.7734627808
12	1.29292020836	-2.75984899966	0.247631410367	6.98474924858	-1.00608717845	0.23669930491	0.209949017559	0.313002404279	-0.329257571416	0.135887273284	0.00276614970343	0.445132293764	0.260041144484	-0.0678198170402	-0.270940144346	0.626392962091	-0.00797138930742	-0.286240520626	0.774091452705	-0.0106238244149	0.658224651222	92.6819705083	75.4253640516	24.2263953944
13	5.43544234974	2.52157679912	1.56642761975	3.91427078163	0.39818451951	4.29322126648	-0.205017630189	-1.58313823729	0.195365423466	0.634544050911	0.217967644343	0.0544106285386	-0.34405693843	-0.675503822369	-0.041483129437	0.520338871074	0.201697021687	-0.0213639085309	0.831968611607	-0.105280671748	0.576003781629	69.4869502022	87.9451938518	30.2356459331
14	6.13609015461	-0.237975376882	-1.2717190944	2.81852928088	2.26592882039	6.52707250008	-0.171256736565	-0.790127917218	0.0955131865455	-0.225108859782	0.228042280693	-0.407500580573	-0.582557876447	-0.21814428461	0.0296683739045	0.665512778332	-0.0102621294696	-0.0155425013252	0.825611430089	-0.117793350839	0.992546801361	76.4006257936	93.8576063132	28.953356404
15	4.94908890338	3.21201458916	-1.29548188533	8.99167022033	-4.32465211062	7.26678510782	0.179916336823	0.00243223440926	0.117240302804	0.14834933598	-0.38624919739	-1.77500948168	0.222828381637	0.951950308679	0.106452313129	0.43254257656	-0.0402381621502	-0.126497800984	0.643422244422	-0.0284204035126	0.817241888878	95.7808117741	78.5629791249	15.4746049533
16	8.90497092521	1.27475223281	2.00642430851	8.23386178182	1.35116190549	2.66488669659	-0.209395039484	0.484357171203	1.48804378125	0.579795698193	-0.554791409918	0.269674646738	-0.540770867557	0.203801557343	0.732055851967	0.608652399976	-0.0297238832207	-0.0365885295289	0.522215329371	0.0780865687695	0.86394346402	68.3893801724	59.828212695	31.5868300736
17	6.00437468588	5.07722621104	-1.17884760257	5.57204930586	-3.12634637948	4.4440653927	-0.549357809216	0.0900882796078	-0.947098094226	-0.370086789976	0.690499947608	-0.477484368717	0.469470567694	-0.445869868552	-0.0242639319591	0.678067315407	-0.0842287004197	-0.106564444877	0.534451355667	0.091704086599	1.00586047768	80.2525555965	53.9473046247	29.8998521058
18	6.88865625013	-0.174187380975	1.98849440913	8.20281080195	3.60111655143	5.4829099903	-0.229420337492	0.590099460848	0.234760258439	0.210441159743	0.248736437642	-0.73647971423	0.52784739946	0.0881519401051	-0.0476752236816	0.607150714455	0.0444324673357	0.102047168842	0.518385945409	0.0676601807119	0.504958194602	64.6168699653	34.9432653605	21.8142713144
19	8.21500105198	0.0895631669624	-5.20664578844	1.53684576094	-0.894861539509	4.23428240525	0.398927816532	-0.800080813819	0.974798703367	0.549227868328	-0.10546982931	-0.190659930296	-0.262795633499	1.47237651735	-0.324978781406	0.716988981126	-0.160405178513	-0.0850007130649	0.697740144286	-0.0141757067232	0.70887966389	76.7500324868	59.521880996	35.9953908339
20	4.22481792379	1.31067971035	0.88214343812	4.70532589039	1.51843033394	6.20533191501	0.0412587436061	-0.197843644823	-0.233601970678	0.135513699069	0.0628645238325	0.0772008414386	0.310866966289	-0.303012375483	-0.0781735629818	0.343127547479	0.0750798589058	-0.138126069661	0.592314420783	0.123469950976	0.789398736139	59.5007598614	80.0908099478	16.0416960299
21	5.01864659026	2.70883308913	1.7770093617	6.60147151714	-0.49574059602	4.42580863019	-0.0935772670829	-0.131700401511	-0.31214096984	-0.865834608283	-0.100321567044	0.554951833431	0.908908446703	-0.547157712681	-0.164160304295	0.601584429321	-0.0209370261703	-0.357354348287	0.533802766662	0.0743217938176	1.02010421345	54.0810682724	77.0066705728	3.68924010574

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 160 through 216 )	C	G	160 - 216	75 - 131
2	2	chain 'C' and (resid 217 through 260 )	C	G	217 - 260	132 - 173
3	3	chain 'C' and (resid 261 through 284 )	C	G	261 - 284	174 - 197
4	4	chain 'D' and (resid 87 through 136 )	D	I	87 - 136	1 - 50
5	5	chain 'D' and (resid 137 through 152 )	D	I	137 - 152	51 - 66
6	6	chain 'D' and (resid 153 through 175 )	D	I	153 - 175	67 - 89
7	7	chain 'D' and (resid 176 through 204 )	D	I	176 - 204	90 - 118
8	8	chain 'D' and (resid 205 through 239 )	D	I	205 - 239	119 - 153
9	9	chain 'D' and (resid 240 through 258 )	D	I	240 - 258	154 - 172
10	10	chain 'D' and (resid 259 through 283 )	D	I	259 - 283	173 - 197
11	11	chain 'A' and (resid 86 through 145 )	A	A	86 - 145	1 - 60
12	12	chain 'A' and (resid 146 through 159 )	A	A	146 - 159	61 - 74
13	13	chain 'A' and (resid 160 through 239 )	A	A	160 - 239	75 - 154
14	14	chain 'A' and (resid 240 through 260 )	A	A	240 - 260	155 - 172
15	15	chain 'A' and (resid 261 through 284 )	A	A	261 - 284	173 - 196
16	16	chain 'B' and (resid 87 through 145 )	B	E	87 - 145	1 - 59
17	17	chain 'B' and (resid 146 through 161 )	B	E	146 - 161	60 - 75
18	18	chain 'B' and (resid 162 through 258 )	B	E	162 - 258	76 - 172
19	19	chain 'B' and (resid 259 through 284 )	B	E	259 - 284	173 - 198
20	20	chain 'C' and (resid 86 through 144 )	C	G	86 - 144	1 - 59
21	21	chain 'C' and (resid 145 through 159 )	C	G	145 - 159	60 - 74

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