PDB-9kea: Crystal structure of LnzB (Streptomyces spp. )

ID or keywords:

Entry

Database: PDB / ID: 9kea

Title

Crystal structure of LnzB (Streptomyces spp. )

Components

FMN-binding negative transcriptional regulator

Keywords

BIOSYNTHETIC PROTEIN / heme-iron dependent / N-N bond formation enzyme

Function / homology

Transcriptional regulator PAI 2-type / Putative FMN-binding domain / FMN-binding split barrel / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / FMN-binding negative transcriptional regulator

Function and homology information

Biological species

Streptomyces parvus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.30000255522 Å

Authors

Zhang, Z.M. / Wang, L.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of LnzB (Streptomyces spp. )
Authors: Zhang, Z.M. / Wang, L.

History

Deposition	Nov 4, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kea.cif.gz	416.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9kea.ent.gz	286.4 KB	Display	PDB format
PDBx/mmJSON format	9kea.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kea_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9kea_full_validation.pdf.gz	2 MB	Display
Data in XML	9kea_validation.xml.gz	43.4 KB	Display
Data in CIF	9kea_validation.cif.gz	56.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ke/9kea ftp://data.pdbj.org/pub/pdb/validation_reports/ke/9kea	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: FMN-binding negative transcriptional regulator

B: FMN-binding negative transcriptional regulator

C: FMN-binding negative transcriptional regulator

D: FMN-binding negative transcriptional regulator

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	107.621, 162.475, 59.032
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	PHE	PHE	chain 'A'	A	A	0 - 44	1 - 45
1	2	LEU	LEU	GLU	GLU	chain 'A'	A	A	64 - 148	65 - 149
1	3	THR	THR	SER	SER	chain 'A'	A	A	151 - 204	152 - 205
1	4	ARG	ARG	SER	SER	chain 'A'	A	A	209 - 221	210 - 222
2	5	SER	SER	PHE	PHE	chain 'B'	B	B	0 - 44	1 - 45
2	6	LEU	LEU	GLU	GLU	chain 'B'	B	B	64 - 148	65 - 149
2	7	THR	THR	SER	SER	chain 'B'	B	B	151 - 204	152 - 205
2	8	ARG	ARG	SER	SER	chain 'B'	B	B	209 - 221	210 - 222
3	9	SER	SER	PHE	PHE	chain 'C'	C	C	0 - 44	1 - 45
3	10	LEU	LEU	GLU	GLU	chain 'C'	C	C	64 - 148	65 - 149
3	11	THR	THR	SER	SER	chain 'C'	C	C	151 - 204	152 - 205
3	12	ARG	ARG	SER	SER	chain 'C'	C	C	209 - 221	210 - 222
4	13	SER	SER	PHE	PHE	chain 'D'	D	D	0 - 44	1 - 45
4	14	LEU	LEU	GLU	GLU	chain 'D'	D	D	64 - 148	65 - 149
4	15	THR	THR	SER	SER	chain 'D'	D	D	151 - 204	152 - 205
4	16	ARG	ARG	SER	SER	chain 'D'	D	D	209 - 221	210 - 222

#1: Protein	FMN-binding negative transcriptional regulator Mass: 24873.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces parvus (bacteria) / Gene: G3I50_12820 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K3RVR3
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.6 Å³/Da / Density % sol: 52.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.4 M Sodium phosphate monobasic, 1.6 M Potassium phosphate dibasic, 0.2 M NaCl and 0.1 M Imidazole, pH8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.14→81.24 Å / Num. obs: 52784 / % possible obs: 91.7 % / Redundancy: 10.2 % / B_iso Wilson estimate: 30.1846899792 Å² / CC_1/2: 0.998 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.14→2.26 Å / Num. unique obs: 52784 / CC_1/2: 0.917

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692+SVN	refinement
Coot		model building
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.30000255522→49.3154042357 Å / SU ML: 0.289884022938 / Cross valid method: FREE R-VALUE / σ(F): 1.32812535602 / Phase error: 26.637262729

	R_factor	Num. reflection	% reflection
R_free	0.241530762396	1694	3.80460415497 %
R_work	0.206399944253	42831	-
obs	0.207769246878	44525	94.9866666667 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.8203812679 Å²

Refinement step

Cycle: LAST / Resolution: 2.30000255522→49.3154042357 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6674	0	15	366	7055

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00876234701214	6867
X-RAY DIFFRACTION	f_angle_d	1.26977843464	9407
X-RAY DIFFRACTION	f_chiral_restr	0.0488569194111	1006
X-RAY DIFFRACTION	f_plane_restr	0.00836545063145	1201
X-RAY DIFFRACTION	f_dihedral_angle_d	15.5966918328	2473

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 (%)
2.301-2.3677	0.294923662249	141	0.279588718789	3551	X-RAY DIFFRACTION	95.9459459459
2.3677-2.4441	0.308353152282	145	0.270299671817	3597	X-RAY DIFFRACTION	97.4225462119
2.4441-2.5315	0.362082259993	143	0.275084053228	3660	X-RAY DIFFRACTION	98.9076723017
2.5315-2.6328	0.296333470472	144	0.254514123223	3660	X-RAY DIFFRACTION	98.9594172737
2.6328-2.7526	0.295897579474	145	0.245881042702	3690	X-RAY DIFFRACTION	98.8911810211
2.7526-2.8977	0.266636933672	146	0.243295540332	3671	X-RAY DIFFRACTION	98.6559834583
2.8977-3.0792	0.294346733806	143	0.238892987956	3669	X-RAY DIFFRACTION	98.1715168684
3.0792-3.317	0.27523710444	142	0.219753581448	3579	X-RAY DIFFRACTION	96.0010319917
3.317-3.6507	0.268613064867	111	0.20797242672	2893	X-RAY DIFFRACTION	76.6717713119
3.6507-4.1787	0.193852460549	134	0.167612117133	3325	X-RAY DIFFRACTION	88.0600814664
4.1787-5.2637	0.161144736643	147	0.145922194451	3687	X-RAY DIFFRACTION	96.25910118
5.2637-49.3154	0.211831952651	153	0.182000569518	3849	X-RAY DIFFRACTION	96.1788031723

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	5.29026407821	0.913910774436	3.79076669133	2.20877766791	-0.553115855798	7.87365739246	-0.274343530325	0.247520589713	-0.334517576276	-0.438416473123	0.22583592652	-0.509429237277	0.455018771306	0.696168814083	-0.0799617793118	0.241178006131	0.0315396923991	0.0817120873994	0.314334285791	0.026114496462	0.776976642128	124.485790946	51.3318496684	54.6381390849
2	2.66816565692	-0.618361791194	0.93309879433	1.96120280241	-0.595449961961	1.45196287406	0.0302544125954	0.225224528384	-0.345722486384	-0.182575559244	-0.0200119186722	-0.102175195777	0.101343946759	0.150510109561	-0.0232523352713	0.213949340718	-0.0115431886082	0.0264367662993	0.194652622529	-0.0567340793207	0.287769578579	108.380007636	54.1551755695	52.2131421836
3	3.30464934204	0.203770133626	0.815395672195	5.65748831944	-0.0478654181716	3.05600763526	-0.127832459937	0.624961925089	-0.565302253882	-0.42157959923	0.0389992129318	-0.0205880677285	0.408907115073	0.0727921267546	0.0310693543711	0.313060723837	-0.059902713665	0.0368037083655	0.419606139432	-0.180370088592	0.418524912036	96.8568392857	46.8488534803	37.534660778
4	1.6032940194	-0.128708670231	-0.175269936108	1.78882095446	-0.571928477236	1.64253021249	0.00401953002811	0.426743807272	-0.157200221191	-0.295932257108	-0.0610506621247	0.108348589918	0.216139475503	-0.102270968303	0.0834243243605	0.290482371504	-0.00691380023547	0.0110645646536	0.210075089934	-0.0918813388851	0.276562978282	99.2034839295	53.9042853424	42.7633612524
5	1.59203902799	1.72063265746	0.680779441892	2.49034295191	1.49132827705	1.45744330518	0.39675446925	-0.275085805545	-1.32405037202	0.120791390129	-0.24407940724	-0.0560967887391	0.34657197533	0.0563328358055	-0.136618954196	0.345487214616	0.0485657749012	-0.0734470267786	0.313624638883	0.0555748536356	0.833309920886	123.818025634	34.791283831	61.5226171149
6	7.32160282524	0.319428826872	-1.0961426918	5.59202678435	-1.09524158879	7.78426590736	-0.328023641189	0.0732687821308	-0.652425657039	-0.375748995475	0.477472229686	0.223402271447	0.428846956275	-0.375416442147	-0.175149479261	0.346156272209	0.0332473684412	-0.033931107943	0.309320069962	-0.0263386887276	0.832349108726	116.655282325	36.0417455651	55.2496599916
7	6.28837491812	0.960766813118	2.70583766023	4.80134556366	1.03193781739	6.57696013837	-0.0422948628389	-0.380772100671	-0.305287963903	0.777051307725	-0.0190009514381	0.561096880808	0.280006389948	-0.701158142463	-0.00762342732008	0.313627026207	0.0230739362332	0.111188909802	0.323139845608	0.0525214607919	0.582414147506	89.3109881815	52.2334014824	61.5866295684
8	2.2376467453	-0.805166060264	0.510787228695	1.78245189096	-0.058718061829	1.35134348227	0.0200569274641	-0.337397973975	-0.2010463236	0.13601677962	0.0197777024001	-0.123029805937	0.0412147479432	-0.116106758563	-0.032311018973	0.270338701935	-0.00307164453514	-0.0252094348879	0.241313739985	0.0128181579553	0.362957115822	108.34600812	55.3219136172	67.8595909115
9	3.85259125928	-2.52750042343	0.130120789441	2.46427523489	0.177007517031	1.77453374856	-0.127245681132	-0.0321852348189	0.715020616482	0.216350638355	-0.00914767763114	-0.0603003644185	-0.15379423898	-0.11078715655	0.0934311687955	0.243884696091	-0.0193255596611	-0.0245349754528	0.18697785894	0.0415955901289	0.232202559012	111.420235459	62.37790419	65.7702773618
10	1.34398997775	0.00117722050209	0.650321417002	0.906509343617	0.356999333211	1.25846592305	0.131846073797	0.0549626071502	-0.420865703256	-0.0412082381424	-0.0870683177969	-0.0398085954652	0.146686491271	-0.058701605302	-0.0263615915327	0.264110276141	-0.0432108726235	0.0374378363729	0.202807201323	-0.0327535701178	0.42184853519	98.7983344802	48.5721681282	57.1692252022
11	1.92330169612	-0.336636318683	0.0494394533769	1.97551380551	0.299562135879	1.36899108816	0.0215648693101	-0.573182554098	-0.519371711838	0.515709591852	0.0193216606349	-0.178484988778	0.289006583563	0.107912443189	-0.0308593213546	0.385103009162	0.00198178679678	-0.0538757219785	0.333078686402	0.139276696111	0.429044527193	115.6489116	50.0344165373	75.846516969
12	4.78859273448	-0.759306763166	2.26969718472	5.00456809278	-0.708020138171	6.33299176992	0.37888189605	-0.103177528701	-0.830145382397	0.148245216287	0.0792774355543	-0.774361392653	0.603153703434	0.098202014929	-0.458891826662	0.344214955413	-0.0672755151892	-0.0927509619428	0.288569143457	0.0371816567432	0.692472364185	92.2701322689	36.1624697845	57.0293769343
13	2.06971829386	-0.278184218051	-0.431623410911	2.59771075031	-0.515564076992	1.54831078391	-0.00200579617688	0.124300775087	-0.407520157133	-0.353378691365	-0.0102031035598	0.138544491828	0.159980420736	-0.225487661621	-0.0328234096246	0.218973596092	0.0189862260956	-0.0347935837899	0.259746416392	-0.0214893273658	0.345622880196	79.9177884206	76.8250012646	52.3002668233
14	0.793926129786	1.21542918302	0.00865696749727	3.16024003166	0.430548950042	0.605183524722	0.0078771221956	0.653624574998	0.339413084443	-0.666215673919	0.172116168829	0.650453997586	0.137769759872	-0.36223791008	-0.183188006476	0.385069846498	-0.0323588097134	-0.0938921506661	0.525789828772	0.0279399317571	0.330036917523	82.1723501696	81.3031467473	41.1116625264
15	2.43730813322	-1.89487522378	1.14188385989	5.77930845385	0.218345993416	0.866970614565	0.0609506540088	0.290486752884	0.287314275549	0.278539268727	-0.0784325073161	-1.23260177747	0.0309042328668	0.103321960672	0.0696898284898	0.187015794619	-0.00544021269614	-0.0250919070288	0.279111856666	0.0417871421573	0.253810517778	88.8945200338	88.2231702956	50.8433944128
16	1.9311328669	0.115818682521	-0.310328556154	1.63061492695	-0.745493161168	1.86138225818	-0.0442588840373	0.137130393162	0.00734891444648	0.112494032929	0.106083350753	0.393927716215	-0.000622488993064	-0.224174914438	-0.0456223437345	0.200932839458	0.00117104922637	-0.0130377004461	0.243139121823	-0.030133312886	0.500604739713	74.6042211135	74.1640959392	59.5043264912
17	4.04343732356	-0.578202757306	-0.367130704468	2.68837317554	-6.69745978124E-5	2.81464808182	-0.207264197745	1.01077454428	0.0164126456993	-0.410982386474	-0.0616858290089	0.706715253732	0.0346080362852	-0.613711371442	0.17950675738	0.409195817942	0.0346861500426	-0.202307986993	0.501785496451	-0.0478881311182	0.404633289301	72.8428474282	91.9239278898	38.0159336817
18	2.0100037451	0.00784873610544	-0.678452771076	1.30451288664	0.133605994954	1.13058340291	0.00232794305003	0.400073739347	0.24636363238	-0.390388690162	-0.0303650255589	0.198567616864	-0.0431226330629	-0.0549976211948	0.0511017081392	0.241307907429	-0.0107632548404	-0.136022635637	0.30649951069	0.0149662605571	0.311162999071	79.976090337	89.6959537601	43.1612222467
19	8.63471423211	-1.13529852854	-0.843961182006	6.5187091712	-1.99378875704	7.73065451729	0.0335358698389	0.11680252999	0.18534291723	0.193098343624	0.22985988715	0.553481613346	-0.229176373231	-0.759502613933	-0.21569953748	0.237617559111	-0.0334672995163	-0.0241590629988	0.388583092134	0.0390856088323	0.608168939679	61.8336380992	67.381604501	59.7952464286
20	7.92560438092	-1.73527795807	-1.34669162625	6.19685601589	-1.12557092911	8.40720559496	-0.186753565279	-0.452133458192	0.453407280091	0.466186571577	-0.309712201482	-0.0280692336234	-0.83966518988	-0.131472042208	0.420797415917	0.314931919928	-0.00688367340135	-0.0541717632135	0.286708817829	-0.0798768263955	0.628370541237	78.6088974122	99.5566548818	62.0041999061
21	1.9147595588	-0.758792932733	0.482509803469	2.50483507057	-0.797568136303	1.1853415107	-0.031974061077	-0.192349818446	-0.0131360094536	0.17805052882	0.0227325331027	0.308905043237	-0.0964046054825	-0.110247344761	0.013621715565	0.166583022941	-0.0162419139172	0.0178675114914	0.229589911456	-0.0393643150495	0.279780165067	80.6552020853	83.4017221439	64.4764611502
22	7.61187555019	0.262813731314	-0.146510733735	4.02294210681	-0.559004210709	3.03541468599	-0.092680305291	-1.19506302846	0.270559577709	0.785638650557	0.109029594364	0.406808127078	-0.12248361763	-0.896646021021	0.047148313839	0.36769544738	-0.00642669483811	0.11835644629	0.488729356706	0.00673029741374	0.339002856807	72.796127468	72.4067728986	79.1402861063
23	2.3508021308	0.0111912776983	0.540642737886	1.9802528844	0.268744455038	1.45323032399	-0.0257066892749	-0.534287935194	-0.291388445432	0.812890662246	0.00495741248111	0.314354625193	0.0408151787268	-0.120248334985	0.0245513046226	0.261081306453	0.0307164432496	0.100068698329	0.369433441758	0.0275538767315	0.350284997887	79.9560064002	74.2800307954	73.8862057535
24	4.94936162273	0.274794056816	0.184204940555	4.134863392	-1.55112762813	4.42786423344	0.116976292729	-0.263766797037	0.374599317769	-0.277178348472	-0.0487341689129	0.559752184484	0.133259369776	-0.207296927432	-0.0362988803731	0.244373108356	0.0347542769275	-0.0491227742422	0.306039191032	-0.0305677114503	0.630753898614	62.6001693999	96.4717824767	57.8389285417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 130 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 131 through 155 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 156 through 184 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 185 through 203 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 204 through 221 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 11 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 77 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 78 through 94 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 95 through 130 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 184 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 185 through 221 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 0 through 44 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 45 through 74 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 75 through 94 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 95 through 130 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 131 through 155 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 156 through 184 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 185 through 221 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 0 through 11 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 12 through 130 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 131 through 155 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 156 through 184 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 185 through 222 )

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