PDB-8c3l: PaaR2 N-terminal domain in complex with nanobody 33

ID or keywords:

Entry

Database: PDB / ID: 8c3l

Title

PaaR2 N-terminal domain in complex with nanobody 33

Components

Nanobody 33
Phage repressor protein CI

Keywords

DNA BINDING PROTEIN / CI repressor / DNA binding / HTH motif / Helix-turn-helix / nanobody complex / nanobody

Function / homology

IODIDE ION / Phage repressor protein CI

Function and homology information

Biological species

Escherichia coli O157:H7 (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59709555301 Å

Authors

Loris, R. / Prolic-Kalinsek, M.

Funding support

Belgium, 1items

Citation

Journal: To be published
Title: PaaR2, the CI equivalent in Escherichia coli O157:H7 cryptic prophage CP-933P
Authors: Prolik-Kalinsek, M. / Volkov, A. / Loris, R.

History

Deposition	Dec 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 15, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8c3l.cif.gz	175.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8c3l.ent.gz	118.2 KB	Display	PDB format
PDBx/mmJSON format	8c3l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8c3l_validation.pdf.gz	451.3 KB	Display	wwPDB validaton report
Full document	8c3l_full_validation.pdf.gz	454.3 KB	Display
Data in XML	8c3l_validation.xml.gz	16.5 KB	Display
Data in CIF	8c3l_validation.cif.gz	23 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c3/8c3l ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c3l	HTTPS FTP

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Related structure data

Related structure data	8c3kC 7nkv C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Phage repressor protein CI

B: Nanobody 33

C: Phage repressor protein CI

D: Nanobody 33

hetero molecules

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

1

A: Phage repressor protein CI

B: Nanobody 33

hetero molecules

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

2

C: Phage repressor protein CI

D: Nanobody 33

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.599, 56.563, 128.292
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Phage repressor protein CI Mass: 7881.091 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs_2279 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XAD6
#2: Antibody	Nanobody 33 Mass: 12821.132 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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 Å³/Da / Density % sol: 38.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M sodium iodide, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 1.59709555301→40 Å / Num. obs: 83789 / % possible obs: 99.2 % / Redundancy: 12.7 % / B_iso Wilson estimate: 25.2000867416 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.066 / R_rim(I) all: 0.069 / Net I/σ(I): 19.02
Reflection shell	Resolution: 1.59709555301→1.69 Å / R_merge(I) obs: 1.719 / Num. unique obs: 6812 / CC_1/2: 0.565 / R_rim(I) all: 1.221 / % possible all: 95.1

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.59709555301→37.1655072961 Å / SU ML: 0.256588152097 / Cross valid method: THROUGHOUT / σ(F): 1.33912132712 / Phase error: 28.0292075939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.254360623879	3797	4.53167518022 %
R_work	0.218600100317	79991	-
obs	0.220244732048	83788	98.4849019124 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.8598419711 Å²

Refinement step

Cycle: LAST / Resolution: 1.59709555301→37.1655072961 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2557	0	17	164	2738

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00576260465058	2677
X-RAY DIFFRACTION	f_angle_d	0.900498551578	3632
X-RAY DIFFRACTION	f_chiral_restr	0.047962772889	393
X-RAY DIFFRACTION	f_plane_restr	0.00567083861153	466
X-RAY DIFFRACTION	f_dihedral_angle_d	11.8187042021	1603

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 (%)
1.5971-1.6173	0.457651167541	100	0.393792337071	2039	X-RAY DIFFRACTION	67.2641509434
1.6173-1.6386	0.445360566857	128	0.352109213182	2740	X-RAY DIFFRACTION	92.3076923077
1.6386-1.661	0.386930084024	144	0.307511926292	3048	X-RAY DIFFRACTION	99.9686814908
1.661-1.6848	0.304418329722	142	0.286199440193	3002	X-RAY DIFFRACTION	100
1.6848-1.7099	0.337578918563	142	0.276197938141	2991	X-RAY DIFFRACTION	99.9680918953
1.7099-1.7366	0.303783456798	137	0.277534676139	3020	X-RAY DIFFRACTION	100
1.7366-1.7651	0.309299335925	143	0.271762642919	3024	X-RAY DIFFRACTION	100
1.7651-1.7955	0.309666060469	143	0.261583139496	2978	X-RAY DIFFRACTION	100
1.7955-1.8282	0.315209935639	144	0.254075656148	3039	X-RAY DIFFRACTION	100
1.8282-1.8634	0.322210093329	141	0.2571974691	2998	X-RAY DIFFRACTION	100
1.8634-1.9014	0.304204568176	144	0.249321033372	3043	X-RAY DIFFRACTION	100
1.9014-1.9427	0.292752795347	140	0.242818492961	2974	X-RAY DIFFRACTION	100
1.9427-1.9879	0.290044504926	141	0.233813933731	3006	X-RAY DIFFRACTION	100
1.9879-2.0376	0.311633258238	141	0.23894574006	3005	X-RAY DIFFRACTION	100
2.0376-2.0927	0.308193415282	144	0.226559740344	3019	X-RAY DIFFRACTION	100
2.0927-2.1543	0.22912527446	143	0.225560779221	2999	X-RAY DIFFRACTION	100
2.1543-2.2238	0.240743595776	142	0.215629251382	2991	X-RAY DIFFRACTION	100
2.2238-2.3033	0.258754342763	143	0.229446565827	3014	X-RAY DIFFRACTION	100
2.3033-2.3955	0.230370575636	142	0.234402239016	3023	X-RAY DIFFRACTION	100
2.3955-2.5045	0.3039181129	142	0.235275128475	3011	X-RAY DIFFRACTION	99.9682942295
2.5045-2.6365	0.31167558625	137	0.236529662904	2984	X-RAY DIFFRACTION	100
2.6365-2.8016	0.244225391291	146	0.230393937261	3021	X-RAY DIFFRACTION	100
2.8016-3.0179	0.233304032093	144	0.219238496569	3015	X-RAY DIFFRACTION	100
3.0179-3.3214	0.207508121155	141	0.208179617276	3003	X-RAY DIFFRACTION	100
3.3214-3.8016	0.224581778562	147	0.1787762142	3024	X-RAY DIFFRACTION	100
3.8016-4.788	0.213947507631	146	0.177937060112	2979	X-RAY DIFFRACTION	100
4.788-37.1655	0.248142915673	150	0.213408402899	3001	X-RAY DIFFRACTION	99.8732171157

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	0.39201779011	0.486679212198	0.100265679923	0.622021000104	0.0148282397662	0.0318923707101	0.153791749378	-0.526159404415	0.408841078425	0.375525517423	-0.157449986122	-0.0472449763681	-0.191480110928	0.434395550665	-0.00103897000108	0.331048116344	0.0779397504042	-0.0319364311134	0.513525690819	-0.0653688992761	0.190153746594	45.6286186578	36.0887975538	126.08648949
2	0.365515961658	-0.379951652052	-0.00954981589446	0.35327093964	-0.0150016556017	-0.0418139996311	0.176900744542	0.159048241892	-0.0750441820644	-0.0453881229202	-0.11176566096	-0.355176059419	-0.0365109639132	-0.00329945042945	5.92772803678E-5	0.217022441107	0.0640877114186	-0.0198184446715	0.265088253569	0.00377436639165	0.353656487443	45.489573023	33.4958859861	114.123389651
3	0.0267010007949	-0.0448777776629	0.115897028779	0.405861384481	-0.568420625248	0.824012185721	-0.109816952019	-0.0740434609316	-0.109630039803	0.486216820038	0.163723010876	-0.214974642187	-0.31126740784	-0.132290268929	0.10763699359	0.225304888984	0.0519531435504	-0.131621278456	0.254467054305	-0.0686280172123	0.275439453375	44.85615368	45.1257798979	119.148445382
4	0.412023757474	-0.294276128737	0.0329150214079	0.352045997797	-0.252132247597	0.322583130039	-0.247565282237	-0.0994507080804	0.117735440122	-0.11251593952	0.2140472656	0.15049218154	-0.152210434911	-0.0785823921476	-6.77897531558E-5	0.196936926992	0.000720608236279	-0.0200081061375	0.191371539591	-0.0013596890103	0.166558361998	23.8312990757	48.0050556576	107.964842818
5	0.106050965756	-0.0654669540972	0.0914261730833	0.136396236158	-0.0394178802006	0.0664214444841	0.0823371726324	0.157439707026	-0.195289578075	0.218960011889	-0.0408391372867	-0.105962819076	-0.0874843910034	-0.0587917628857	0.000602944675184	0.194105593757	0.0236978616705	0.00136615051941	0.254889244751	0.00739687218655	0.200242013003	29.360109495	42.4070673811	113.222530777
6	0.154039062301	-0.131378414352	0.107403924759	0.367387727269	0.265829926915	0.421640296931	-0.0533531991635	0.0463835235077	0.0383865622088	-0.240555926996	0.185084247837	0.106063359885	0.270029549377	0.0347048718096	-0.000124790856941	0.167274305922	0.0197522700333	-0.0135504027998	0.235774348446	0.0287159035623	0.217487857224	29.5017788066	37.3555829817	112.480284777
7	0.468199838257	0.0744058961333	0.256846063111	0.0407189314874	-0.00178631135326	0.29048736026	0.00220159185218	0.308673724888	-0.0756747854678	-0.1719424333	0.00570445801991	-0.164982341004	0.0100051265277	0.116925146981	0.000116292108101	0.246274724972	-0.0015436823089	0.0126670638539	0.222650204178	0.00842692888802	0.217369732345	27.925261899	41.0668760068	103.613512342
8	0.150682442902	-0.0052755320228	-0.000848963497491	0.00123239899672	-0.0049069939824	-0.00100639879658	0.0901866035472	0.127400482874	-0.506748685182	-0.0316526834746	0.248758496359	0.362009593706	0.39536313145	0.0221106047533	0.00717779246316	0.375358676296	-0.0289327898452	0.00382013310698	0.273076952025	0.0811964989478	0.318875588114	16.8864393192	32.274313326	105.672825956
9	0.0815374634112	-0.119490685758	-0.0343454449967	0.128707336438	0.0659796599339	0.109390891712	-0.361667635857	-0.0588809949506	0.15985611356	-0.120873912669	0.229398539337	0.0943953304626	-0.122554203622	0.00750040952809	0.000404454711403	0.223660505051	0.0475907180601	0.00678698448953	0.251850996292	0.0286655290913	0.216487702796	26.4388992507	46.1729432017	116.960772492
10	0.04400901031	0.0146210549861	-0.179516980045	0.14612516261	0.418450588523	2.41190644855	-0.302656161358	-0.198441726678	0.120599789038	-0.130093370506	0.0990113786654	-0.0479263927301	0.659922263156	-0.573667710045	-0.0392435849459	0.260759652721	-0.0611640527867	-0.0641544461553	0.317031761842	0.0369750534017	0.293931904168	12.7224837076	39.5724151879	109.25288092
11	0.160672746792	-0.116043835372	0.0536960594305	0.0982252852366	-0.0267894278825	0.050331263775	-0.0148190494709	0.307109759457	-0.15046945544	-0.236385607177	-0.107707064794	0.0604119400271	0.0262734105274	0.0941559379079	0.000232620886448	0.332344749844	-0.0498005705052	0.00832413639241	0.329937259907	-0.0017786117319	0.208604914714	39.495741181	49.0895835591	67.9065304008
12	0.20914746207	0.154154003056	0.149040111091	0.346268650287	-0.180712854814	0.280166599457	0.137528501742	0.0619398330316	0.0909605941537	0.242566064531	-0.0769498451539	-0.19994637821	-0.479177404929	0.125139825786	0.00186111221168	0.266841203092	-0.0869591604946	0.022946461337	0.317138996282	-0.015942258564	0.269197468607	41.5617026683	49.754867239	78.3446067945
13	0.0412492494522	-0.0460830502269	0.0104458273097	0.0177605674744	-0.0404015434528	0.045906481268	-0.114519019054	0.0995220682586	-0.265274550212	-0.0573528024858	0.0177284708724	-0.30359327007	0.0142496278337	0.0702039212813	-0.000118481644257	0.260632217189	-0.0716230847756	0.0293557545631	0.328287907627	-0.0387697714688	0.259100782491	39.2966888739	39.0827345365	71.6135981553
14	0.00767300045613	0.163463478892	0.159024365914	0.475254183278	0.159425600587	0.458662039698	-0.114573667171	0.0965213482546	-0.0549580286363	0.279668221841	0.0994008789328	0.0202742989188	0.304541461333	-0.0731463407043	-0.000123990150088	0.23715153252	-0.0227578587222	0.0223861446358	0.195127717444	0.0338995498933	0.217713116828	20.7253203706	34.3159428704	85.8063516266
15	0.124539349821	0.114722282886	-0.120492890206	0.16318359942	0.0719802833107	0.394443891786	-0.178272688013	-0.259569852546	0.0197984016126	-0.157400642	0.328361974719	-0.0683722560176	0.208936234041	-0.467648431561	0.00876021796525	0.247533499916	-0.0253268012212	0.00186269642558	0.201088353035	-0.00831240536088	0.213137513667	25.3939433329	40.5843856361	80.2983669399
16	0.118108673002	0.126525018206	0.000132515655863	0.153114701248	0.0658085177138	0.0899213768435	0.403365023858	0.512570092633	-0.0667062297531	-0.243095351628	-0.143455922758	0.256899805096	-0.0797005044299	0.0745620209081	-0.000687158743032	0.25087448105	0.0501643141199	-0.00542297241608	0.215911141646	0.0456208321599	0.243323744365	19.9937367825	47.3036528883	78.9426889091
17	0.165661200144	0.166765104799	-0.0882323258543	0.14673509258	-0.0785599241928	0.0862763450412	0.206923135315	-0.131855152108	-0.0374601094804	0.14472720158	-0.226172807528	0.0859401538646	-0.35157286664	0.254395266276	-0.000658411847294	0.256381104342	0.00134897568421	0.000980345689183	0.179615307145	0.0142370654437	0.236582918831	30.1058250893	46.2066346536	87.8042823421
18	0.19241969164	0.103059606168	0.0260284629913	0.0694363002952	-0.0250136894086	0.0758932757658	0.0668212623956	0.143440895577	-0.458187771712	0.486507183292	0.0759707974896	-0.0182496879235	0.374500665458	0.15440116332	-0.000670764021102	0.349920232639	0.000150037860446	-0.0200557824829	0.218115810668	-0.0313034439532	0.361860480316	29.0810891136	34.7883637116	89.9971668852
19	0.166853521061	0.30035662914	-0.121070861136	0.567606785101	-0.378068038253	0.373274546024	-0.0806165232118	-0.0947109706037	0.000326141403758	0.0315993364526	0.121773709423	-0.0132622927194	0.00112237833208	0.026610798115	1.14487372474E-5	0.237487565658	-0.0100318829546	-0.0116791185019	0.178728873648	0.0268645530759	0.193618302937	20.1858644668	40.4508306324	83.5138950442
20	0.0233879313928	-0.0191825612259	0.00128317406117	0.0424160267285	0.0161629119431	0.0258562038533	0.168770076884	0.0427200788147	0.254210752485	-0.283852269137	-0.0267716669111	0.164458042444	0.0227277815323	-0.402210610787	-0.000151103120523	0.212841590805	0.0100296006972	0.0544229503734	0.327580303428	0.0200436094996	0.349558688883	9.51214867438	42.9962130459	87.5308680378

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 59 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 30 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 31 through 39 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 40 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 90 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 91 through 104 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 105 through 111 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 15 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 16 through 39 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 40 through 59 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 30 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 31 through 39 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 40 through 51 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 52 through 66 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 67 through 76 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 77 through 104 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 105 through 111 )

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