PDB-9nli: GloR, native, unmodified

ID or keywords:

Entry

Database: PDB / ID: 9nli

Title

GloR, native, unmodified

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: 2.6 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	9nli.cif.gz	200.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9nli.ent.gz	134.3 KB	Display	PDB format
PDBx/mmJSON format	9nli.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/9nli ftp://data.pdbj.org/pub/pdb/validation_reports/nl/9nli	HTTPS FTP

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Related structure data

Related structure data	9nlmC 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

44.7 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)	99.945, 117.303, 34.290
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	LysR family transcriptional regulator Mass: 22339.455 Da / Num. of mol.: 2 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
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4% Tacsimate pH 8.0, 20% PEG3350 / Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→39.1 Å / Num. obs: 13091 / % possible obs: 99.9 % / Redundancy: 6.9 % / B_iso Wilson estimate: 51.63 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.073 / R_rim(I) all: 0.142 / Χ²: 0.97 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.6→2.72 Å / Redundancy: 7.2 % / R_merge(I) obs: 1.132 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1556 / CC_1/2: 0.855 / R_pim(I) all: 0.668 / R_rim(I) all: 1.317 / Χ²: 0.98 / % possible all: 100

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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 / Resolution: 2.6→38.04 Å / SU ML: 0.4241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.7019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.3004	1301	10.01 %
R_work	0.2339	11696	-
obs	0.2406	12997	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: 64.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→38.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3110	0	0	0	3110

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	3198
X-RAY DIFFRACTION	f_angle_d	1.0502	4352
X-RAY DIFFRACTION	f_chiral_restr	0.0576	481
X-RAY DIFFRACTION	f_plane_restr	0.0113	579
X-RAY DIFFRACTION	f_dihedral_angle_d	19.3761	1186

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 (%)
2.6-2.7	0.4857	139	0.3807	1254	X-RAY DIFFRACTION	99.64
2.7-2.83	0.3737	144	0.3197	1283	X-RAY DIFFRACTION	99.17
2.83-2.98	0.3951	139	0.3261	1262	X-RAY DIFFRACTION	99.86
2.98-3.16	0.4267	145	0.3246	1281	X-RAY DIFFRACTION	99.3
3.16-3.41	0.3756	141	0.2797	1283	X-RAY DIFFRACTION	99.16
3.41-3.75	0.3263	144	0.2427	1295	X-RAY DIFFRACTION	99.79
3.75-4.29	0.2734	146	0.1969	1308	X-RAY DIFFRACTION	99.86
4.29-5.4	0.2078	147	0.1729	1317	X-RAY DIFFRACTION	99.73
5.41-38.04	0.2333	156	0.1884	1413	X-RAY DIFFRACTION	98.99

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	0.40070342251	0.164910418285	0.0324265442512	0.0847314738959	0.0094511823895	-0.016827575402	0.124012919678	-0.1907541214	0.173894252167	-0.0800281443421	-0.240775471156	0.0677940133847	0.0412534601605	0.0354679118201	-0.00373427469397	0.38841502123	-0.116294390983	-0.0509813102681	0.343616831299	0.29515356134	0.329435128743	24.5421258233	16.0362876959	3.76939028217
2	0.025937341767	0.0179502463147	-0.00177512556819	0.0296771965375	0.0163747601714	0.00403246864273	0.0376937817511	0.210652964165	0.24294850585	-0.0881339135133	-0.0148315271042	-0.0743517684647	0.180960202871	0.0744017220951	0.000648942114747	0.390603502071	0.125108738258	-0.0116440493601	0.423944173548	0.172789434037	0.381718512827	21.7812484447	23.6068760644	-8.66667840343
3	0.0202976414792	0.00115751237889	-0.0132559456678	-0.0064584859678	0.000362480067769	0.00126934513766	0.00296249237925	0.283768640973	-0.180733983506	-0.00101644428437	-0.0937673362925	0.0804268724325	-0.44700837871	-0.0932567765805	-0.000384021000075	0.396915849769	0.0666849774161	0.0330952121432	0.577474401231	0.147686715696	0.353125432082	11.672798604	25.7924596466	-2.78821932525
4	0.0387614298541	-0.0282518592127	0.00947080689545	0.0662316873202	-0.0583153183298	0.0578496870224	0.260719705712	0.0561347854928	0.438687736248	-0.100211461553	-0.081918063482	0.274075162418	-0.0678875115018	-0.0525636630062	0.000235961966193	0.506048302307	-0.0487371893799	0.129480181008	0.479983259956	-0.0134052763684	0.615721052022	25.15840596	46.8372895776	8.87127853269
5	0.0023118461675	-0.00206776359796	-0.0018098480389	0.0010587007782	0.00392914197724	0.000149584237461	-0.0956284560149	0.0217846157491	0.0510294153603	-0.0778487921805	0.0771043669077	0.143094646129	0.021455045892	-0.140919004424	7.36870467455E-6	0.376354146714	0.0458169066728	-0.00840957495425	0.701598936315	0.0737507787842	0.766539640166	18.2281074726	46.2076060445	0.589135326365
6	0.0561155168102	0.0199446665186	0.0555361672351	0.107137587953	-0.00992119341485	0.0283842035464	0.161905898748	-0.0872493389038	0.194167358088	0.348509370589	-0.363143763565	0.075943087523	0.197958985551	0.133046053435	0.000107777603772	0.338608061825	0.0244348302503	0.0994549876959	0.2905496818	0.0241335707916	0.385571750589	27.4547163585	42.2898772101	11.230567983
7	0.372830696685	0.0683833323243	-0.0549174625298	0.0384865954137	0.00935407592108	0.0341978784578	0.141273226015	-0.21430186272	0.34074391316	-0.0302013980171	-0.0160908518275	0.360172364305	-0.0180853280495	-0.213202717397	0.0266851103535	0.309462868206	0.0459490402613	-0.0504397090711	0.253017563012	0.190221982026	0.351912312075	14.3353218768	17.0250648581	-0.900874872639
8	0.034997377228	0.0151982488215	-0.0179392166641	-0.0017189237478	-0.0112570384796	0.0255117036557	-0.0265765083507	-0.375132401087	-0.0349256749183	0.161800773805	-0.0234113688621	-0.0984487982788	0.150026383123	-0.084980036687	0.000338636723604	0.384535367167	-0.0684312177021	-0.0367860473628	0.640588775115	0.202717881122	0.425774084396	43.0337916063	41.5037059419	5.88133356351
9	0.0807438384044	0.0560499988333	-0.0179913401994	0.0238914228772	0.00997973894376	-0.00093426647924	0.0106256018727	0.22526466959	-0.0658744823365	-0.0945734240167	-0.209368808391	0.23100376912	0.163275246728	0.186219179925	0.000205109462585	0.371902135753	-0.00472592809622	-0.013299506431	0.392056905018	0.163682597749	0.344283727505	42.2579912457	37.9649787842	-5.63207638394
10	0.532179742255	-0.44479469725	-0.2068573264	0.39613123852	0.348921302013	1.4362108903	0.523909646383	0.0453483521376	-0.149714686066	0.277971112614	0.150631462062	-0.389050902703	-0.125451019947	0.0196883782238	1.23784235552	0.249707095051	0.0332710665528	-0.273225234321	0.394224502105	0.363326328795	0.374703747943	48.078303469	19.447490919	6.03502884277
11	0.03544496274	0.0358928503268	0.0470150102783	0.0943395123006	0.0664308058824	0.046686845397	0.0329703637709	0.0326678978626	-0.483370907664	-0.0440455130512	-0.157911258791	-0.200576861271	-0.272673882518	0.0319709908966	-0.000690160184554	0.391006430137	0.028856913355	0.0200427253063	0.46273056223	0.197540125926	0.550630399117	39.3146521544	14.0429093451	4.4939173796
12	0.0014997877946	0.0162268710173	-0.00610655754027	0.0743515817649	-0.0157991882003	0.0134665642558	0.329927661324	-0.046897010436	0.013063202551	0.290647001322	-0.108567433956	-0.401436990485	-0.129247747432	-0.0182458753329	-0.00171367808508	0.478802457943	-0.0731077466542	-0.0992563773579	0.72655780053	0.102878150596	0.663517178655	42.3105956672	20.361710615	15.5133686725
13	0.0604625371767	0.000943872628567	-0.00803511236913	0.0476931756036	0.0424996472589	0.0291109099199	-0.121365023426	-0.058266293054	-0.196155563826	0.308423304208	0.140589777409	-0.370624961282	0.219772600674	-0.0348288611654	-7.93250852359E-5	0.531098153231	-0.00948979862591	-0.0385754038153	0.585394487502	0.127496507268	0.435023146581	52.0086879585	41.6212698687	-1.01632058865

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 'A' and (resid 85 through 126 )	A	A	85 - 126	1 - 42
2	2	chain 'A' and (resid 127 through 145 )	A	A	127 - 145	43 - 61
3	3	chain 'A' and (resid 146 through 161 )	A	A	146 - 161	62 - 77
4	4	chain 'A' and (resid 162 through 193 )	A	A	162 - 193	78 - 109
5	5	chain 'A' and (resid 194 through 203 )	A	A	194 - 203	110 - 119
6	6	chain 'A' and (resid 204 through 258 )	A	A	204 - 258	120 - 174
7	7	chain 'A' and (resid 259 through 284 )	A	A	259 - 284	175 - 200
8	8	chain 'B' and (resid 86 through 114 )	B	B	86 - 114	1 - 29
9	9	chain 'B' and (resid 115 through 145 )	B	B	115 - 145	30 - 60
10	10	chain 'B' and (resid 146 through 182 )	B	B	146 - 182	61 - 97
11	11	chain 'B' and (resid 183 through 234 )	B	B	183 - 234	98 - 149
12	12	chain 'B' and (resid 235 through 258 )	B	B	235 - 258	150 - 173
13	13	chain 'B' and (resid 259 through 284 )	B	B	259 - 284	174 - 199

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