PDB-8efz: Crystal structure of CcNikZ-II, apoprotein

ID or keywords:

Entry

Database: PDB / ID: 8efz

Title

Crystal structure of CcNikZ-II, apoprotein

Components

Extracellular solute-binding protein family 5

Keywords

TRANSPORT PROTEIN / NICKEL IMPORT / METAL TRANSPORT / ABC-TYPE TRANSPORT / SUBSTRATE BINDING PROTEIN / SBP PROTEIN

Function / homology

Function and homology information

ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
Similarity search - Function

Biological species

Clostridium carboxidivorans P7 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Stogios, P.J. / Evdokimova, E. / Diep, P. / Yakunin, A. / Mahadevan, K. / Savchenko, A.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of CcNikZ-II, apoprotein
Authors: Diep, P.

History

Deposition	Sep 10, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8efz.cif.gz	448.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8efz.ent.gz	326.5 KB	Display	PDB format
PDBx/mmJSON format	8efz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8efz_validation.pdf.gz	446.3 KB	Display	wwPDB validaton report
Full document	8efz_full_validation.pdf.gz	467.3 KB	Display
Data in XML	8efz_validation.xml.gz	36.9 KB	Display
Data in CIF	8efz_validation.cif.gz	50.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/8efz ftp://data.pdbj.org/pub/pdb/validation_reports/ef/8efz	HTTPS FTP

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Related structure data

Related structure data	4oetS S: Starting model for refinement
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
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Extracellular solute-binding protein family 5

B: Extracellular solute-binding protein family 5

hetero molecules

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

1

A: Extracellular solute-binding protein family 5

hetero molecules

defined by author
56.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Extracellular solute-binding protein family 5

hetero molecules

defined by author
56.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.606, 110.942, 73.686
Angle α, β, γ (deg.)	90.000, 113.720, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Extracellular solute-binding protein family 5 Mass: 56686.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium carboxidivorans P7 (bacteria) Gene: CcarbDRAFT_1393 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: C6PRH6
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.43 Å³/Da / Density % sol: 49.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30 mg/mL protein and reservoir solution 0.1 M Hepes pH 7.5, 30% (w/v) polyethylene glycol 1000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.38→30 Å / Num. obs: 40340 / % possible obs: 93.9 % / Redundancy: 4.2 % / CC_1/2: 0.99 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.057 / Net I/σ(I): 20.66
Reflection shell	Resolution: 2.38→2.44 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 1752 / CC_1/2: 0.652 / R_pim(I) all: 0.267 / % possible all: 81.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MrBUMP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OET

4oet

Resolution: 2.38→29.71 Å / Cross valid method: FREE R-VALUE / σ(F): 0.65 / Phase error: 29.7277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	2057	5.27 %	RANDOM
R_work	0.2221	37001	-	-
obs	0.2284	39058	90.01 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 51.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→29.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7781	0	2	171	7954

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	7952
X-RAY DIFFRACTION	f_angle_d	0.5446	10716
X-RAY DIFFRACTION	f_chiral_restr	0.0442	1141
X-RAY DIFFRACTION	f_plane_restr	0.0033	1374
X-RAY DIFFRACTION	f_dihedral_angle_d	17.9511	2976

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 (%)
2.38-2.44	0.3637	91	0.3328	1775	X-RAY DIFFRACTION	58.01
2.44-2.51	0.3594	123	0.3293	2400	X-RAY DIFFRACTION	77.72
2.51-2.58	0.3483	131	0.3103	2530	X-RAY DIFFRACTION	82.49
2.58-2.66	0.3519	137	0.2978	2658	X-RAY DIFFRACTION	85.19
2.66-2.76	0.3005	138	0.2816	2610	X-RAY DIFFRACTION	84.99
2.76-2.87	0.305	139	0.2744	2662	X-RAY DIFFRACTION	86.04
2.87-3	0.2812	143	0.2791	2667	X-RAY DIFFRACTION	86.48
3-3.16	0.3089	148	0.2618	2747	X-RAY DIFFRACTION	88.5
3.16-3.35	0.2465	148	0.2451	2793	X-RAY DIFFRACTION	89.58
3.35-3.61	0.2543	145	0.2387	2778	X-RAY DIFFRACTION	90.28
3.61-3.98	0.2596	150	0.2135	2830	X-RAY DIFFRACTION	91.06
3.98-4.55	0.2237	152	0.193	2867	X-RAY DIFFRACTION	91.98
4.55-5.72	0.2289	152	0.1778	2902	X-RAY DIFFRACTION	92.95
5.73-29.71	0.2511	152	0.1903	2890	X-RAY DIFFRACTION	91.34

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	2.63814244684	0.0243001184646	-0.361005119455	0.849683157883	-0.116067219299	0.337562096072	-0.147337158077	0.163926836048	-0.0745973790545	-0.0502378982288	0.135628025205	0.0135047394179	0.0250301163742	0.118382777812	0.0247736685262	0.302139687317	-0.0297394848443	-0.0653230832753	0.530832321199	-0.0390448066356	0.206516782967	12.0132344935	-8.84664115398	-43.5540588417
2	1.92359419467	0.344458279348	2.37969562112	4.7571521708	1.12717123633	2.98637447228	0.141924640434	-0.154701544264	-0.0378426502501	0.510303188025	-0.172789399983	-0.0637775114342	0.00376645759515	0.267478367128	0.035851241333	0.280736753586	-0.0177328556014	0.0059736699041	0.594883433463	0.0293823931961	0.262163176068	22.4342131675	-4.34955790854	-34.6426809679
3	1.52807301706	-1.21151997344	0.0321991508398	1.9334030595	-1.44385660361	3.2799599538	0.0218022034562	0.356721681126	0.119905415414	-0.0468722966585	0.182146659729	0.147651569511	-0.11885641461	0.297244078881	-0.190888885795	0.291763568326	-0.0458946293091	-0.0801390995843	0.55672473223	-0.0270159384752	0.205421959471	13.6754984086	0.976735111015	-41.5338460738
4	1.70315805012	0.471758702191	0.401335461612	2.10707800236	-0.264964577741	3.23098518269	0.0435642546671	0.178815336779	0.271023021276	-0.150725062567	0.163362625029	0.387445212051	0.0239569958124	-0.155251117174	-0.164215615853	0.257303514153	0.0152674926093	-0.0946898946112	0.439076904603	0.000285529486987	0.274885191069	-7.78906159844	-5.94512121283	-47.2918528752
5	0.943871596324	-0.206560709833	-0.483848771051	0.973035520847	-0.404845099206	2.71971918814	0.0893116691547	-0.487328625936	-0.159953939892	0.0848023677743	0.103320088841	0.204111036967	0.37654619384	-0.330267047376	-0.162965374901	0.357042967928	-0.0788042703247	-0.0131322660216	0.567905824393	0.0625554803553	0.293756542624	-6.98199293263	-19.5762954996	-15.4382738065
6	5.69472124432	-0.890294923204	-1.84891561297	4.6306563803	2.92018800341	2.17331349273	0.219402002091	0.455242347514	0.0527080617663	-0.263688679708	0.158476829694	-0.173235657791	0.0113328546624	-0.192499741394	-0.443902513763	0.329748790379	-0.0185430731892	-0.0497391321994	0.558901171699	0.090848593761	0.332605578573	-13.8347231784	-9.42358558476	-15.4818001972
7	2.15214652346	0.539328010692	0.389915640927	0.902454586595	-0.383140979485	3.68541507617	0.203855670907	-0.400373665324	-0.3278635377	-0.00327972485862	-0.053209551273	0.0074297357052	0.24026229501	0.0217348701993	-0.118781126061	0.283120689306	0.00579706319855	-0.0222910173778	0.429234805124	0.0186251531844	0.259006839136	3.80802810744	-15.8940467091	-26.9133483091
8	0.401914209236	-0.288221136243	-0.0488889846196	1.44582277245	0.412992114556	1.23626484951	0.0409672112417	0.226956298739	0.0674463700087	0.0143890891571	0.0543477897578	-0.0668577851104	0.0419604385907	0.127599689821	-0.100756889574	0.268373002035	0.00230816610944	-0.0291312818227	0.631324679628	-0.0310131838541	0.294274072716	7.67071115284	-44.2923578528	-69.9706243916
9	2.8413749829	-2.6897077329	-0.00851725831588	6.18047460772	-2.77187603701	2.90329753299	0.268160467466	0.214560975524	-0.0486336640117	-0.200904673909	-0.0702463539399	0.161525489535	0.0463344186548	0.341604376035	-0.180456805969	0.274308674906	-0.0603995780361	-0.0726556899803	0.735059637349	-0.0829738259288	0.258127289864	8.37279304265	-47.20760441	-76.0609628374
10	2.00629463514	-0.713318273709	0.20169903762	0.690805140055	-0.0392114884931	1.51049395371	-0.17278536485	-0.0589095939399	0.10101952386	0.170538131679	0.0642217198828	-0.00929875382143	-0.0261146948364	-0.0639916782082	0.102748216356	0.28416778565	0.00322713472312	-0.0410837395677	0.352966615873	-0.0223185086008	0.268726888742	-5.40028480546	-40.4168855474	-52.9973822416
11	1.12064420923	-1.00893324207	0.149814408817	0.935791073316	-0.340027526715	1.01590549697	-0.2372272208	0.000163322692018	0.296011316284	0.438885611557	0.123191493278	-0.0358309054458	-0.276126373894	-0.30024150762	0.090773684023	0.60660924304	0.113246037158	-0.0311191080491	0.437294080442	-0.02502374476	0.525740473066	-25.3611528266	-24.9698507633	-64.3948453133
12	4.30240139695	1.45635327516	-0.249982226491	2.80164980145	0.546548295243	3.28270778077	0.0235213700919	0.012831390178	0.483245776611	0.323894384187	-0.0435159781343	0.0761815446179	0.232582877667	0.0894855035805	-0.0188819975907	0.404919174682	0.0446055283166	0.0391192088633	0.48446957379	-0.0065098056749	0.282987905923	-31.5169147973	-39.6687587031	-57.2746863203
13	9.35125646822	4.91331654812	-0.843496268076	6.4345796593	1.50551043034	5.42173068816	-0.284234903587	-0.32134284003	-0.722402875542	0.986210942291	0.427406079753	0.183152123897	0.0320187824622	-0.441675016682	-0.0631666649206	0.524185690974	0.189147238039	0.0841006093616	0.692458755834	0.079865492356	0.348133263739	-23.0459857986	-47.27153359	-60.1821875176
14	6.1593226015	0.0329119555522	1.50040212601	0.221827284154	-0.600746145864	5.5845089042	0.341519719583	1.00603836339	0.0899756640878	-0.388669905279	-0.241059278914	-0.199295029422	0.827737643754	0.152683510695	-0.102129719	0.380078067205	0.128124094653	-0.0295892960676	0.626342347224	-0.0267840484608	0.339269410665	-12.2324656454	-36.237702321	-76.0801615325
15	4.09439045408	-0.229014901637	0.289969841201	1.06509798969	-0.690252659538	3.25798839781	-0.19620913928	-0.0160033708227	0.163656835318	0.0169268596052	0.19187494565	0.0241329181483	-0.310792217361	-0.209856444734	0.0368597801817	0.288161164986	0.0104350065672	-0.0439522034938	0.216981490744	-0.0474914552798	0.281292370431	-4.65491969226	-31.5971108038	-60.731876297

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 11 through 86 )	A	A	11 - 86	1 - 76
2	2	chain 'A' and (resid 87 through 132 )	A	A	87 - 132	77 - 122
3	3	chain 'A' and (resid 133 through 168 )	A	A	133 - 168	123 - 158
4	4	chain 'A' and (resid 169 through 233 )	A	A	169 - 233	159 - 223
5	5	chain 'A' and (resid 234 through 337 )	A	A	234 - 337	224 - 323
6	6	chain 'A' and (resid 338 through 373 )	A	A	338 - 373	324 - 359
7	7	chain 'A' and (resid 374 through 497 )	A	A	374 - 497	360 - 479
8	8	chain 'B' and (resid 11 through 118 )	B	B	11 - 118	1 - 108
9	9	chain 'B' and (resid 119 through 157 )	B	B	119 - 157	109 - 147
10	10	chain 'B' and (resid 158 through 293 )	B	B	158 - 293	148 - 283
11	11	chain 'B' and (resid 294 through 320 )	B	B	294 - 320	284 - 310
12	12	chain 'B' and (resid 321 through 364 )	B	B	321 - 364	311 - 351
13	13	chain 'B' and (resid 365 through 390 )	B	B	365 - 390	352 - 377
14	14	chain 'B' and (resid 391 through 435 )	B	B	391 - 435	378 - 422
15	15	chain 'B' and (resid 436 through 496 )	B	B	436 - 496	423 - 483

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