PDB-7mpm: Bartonella henselae NrnC bound to pAA

ID or keywords:

Entry

Database: PDB / ID: 7mpm

Title

Bartonella henselae NrnC bound to pAA

Components

5'-phosphorylated AA
NanoRNase C

Keywords

RNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex

Function / homology

Function and homology information

nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding
Similarity search - Function

Biological species

Bartonella henselae (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Lormand, J.D. / Sondermann, H.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2021
Title: Structural characterization of NrnC identifies unifying features of dinucleotidases.
Authors: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /

Abstract: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...

History

Deposition	May 4, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	Sep 29, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7mpm.cif.gz	853.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7mpm.ent.gz	584.7 KB	Display	PDB format
PDBx/mmJSON format	7mpm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7mpm_validation.pdf.gz	484.9 KB	Display	wwPDB validaton report
Full document	7mpm_full_validation.pdf.gz	492.9 KB	Display
Data in XML	7mpm_validation.xml.gz	79.2 KB	Display
Data in CIF	7mpm_validation.cif.gz	118.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mp/7mpm ftp://data.pdbj.org/pub/pdb/validation_reports/mp/7mpm	HTTPS FTP

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Related structure data

Related structure data	23941C 23942C 23943C 23944C 23945C 23946C 23947C 23948C 7mplC 7mpnC 7mpoC 7mppC 7mpqC 7mprC 7mpsC 7mptC 7mpuC 7mqbC 7mqcC 7mqdC 7mqeC 7mqfC 7mqgC 7mqhC 7mqiC 1yt3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7mpl-d 7mpn-d 7mpp-d 7mqc-d 7mqh-d 7mqb-d 7mqe-d 7mpq-d 7mqf-d 7mqi-d Search similar-shape structures by Omokage search (details) 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	#3 - Mar 2000 DNA Polymerase similarity (3)

Deposited unit

A: NanoRNase C

B: 5'-phosphorylated AA

C: NanoRNase C

D: 5'-phosphorylated AA

E: NanoRNase C

F: 5'-phosphorylated AA

G: NanoRNase C

H: 5'-phosphorylated AA

I: NanoRNase C

J: 5'-phosphorylated AA

K: NanoRNase C

L: 5'-phosphorylated AA

M: NanoRNase C

N: 5'-phosphorylated AA

O: NanoRNase C

P: 5'-phosphorylated AA

192 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	70.777, 127.472, 128.588
Angle α, β, γ (deg.)	90.000, 95.286, 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	NanoRNase C Mass: 23446.725 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5MEI1
#2: RNA chain	5'-phosphorylated AA Mass: 613.454 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2043 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.5 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Succinic acid; 10% PEG 3,350; 20% xylitol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.0001 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0001 Å / Relative weight: 1
Reflection	Resolution: 1.95→43.48 Å / Num. obs: 165258 / % possible obs: 99.68 % / Redundancy: 3.7 % / B_iso Wilson estimate: 26.42 Å² / CC_1/2: 0.997 / Net I/σ(I): 11.98
Reflection shell	Resolution: 1.95→2.02 Å / Num. unique obs: 16396 / CC_1/2: 0.775

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
Aimless		data scaling
pointless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3

Resolution: 1.95→43.48 Å / SU ML: 0.1694 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1796	2000	1.21 %
R_work	0.1451	163258	-
obs	0.1455	165258	99.61 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→43.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13042	360	0	2043	15445

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14087
X-RAY DIFFRACTION	f_angle_d	0.7602	19231
X-RAY DIFFRACTION	f_chiral_restr	0.0546	2204
X-RAY DIFFRACTION	f_plane_restr	0.0045	2419
X-RAY DIFFRACTION	f_dihedral_angle_d	18.9949	5349

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 (%)
1.95-2	0.2674	140	0.2405	11459	X-RAY DIFFRACTION	98.41
2-2.05	0.2558	143	0.2063	11658	X-RAY DIFFRACTION	99.53
2.05-2.11	0.2533	142	0.1846	11590	X-RAY DIFFRACTION	99.63
2.11-2.18	0.1959	143	0.1661	11656	X-RAY DIFFRACTION	99.87
2.18-2.26	0.1811	142	0.1561	11643	X-RAY DIFFRACTION	99.86
2.26-2.35	0.1954	144	0.1502	11713	X-RAY DIFFRACTION	99.87
2.35-2.45	0.2036	143	0.1526	11661	X-RAY DIFFRACTION	99.9
2.45-2.58	0.1631	142	0.1452	11631	X-RAY DIFFRACTION	99.81
2.58-2.74	0.184	144	0.1476	11696	X-RAY DIFFRACTION	99.71
2.74-2.96	0.1726	143	0.1476	11677	X-RAY DIFFRACTION	99.78
2.96-3.25	0.1951	142	0.1464	11661	X-RAY DIFFRACTION	99.7
3.25-3.72	0.1653	144	0.1326	11668	X-RAY DIFFRACTION	99.21
3.72-4.69	0.1507	142	0.1135	11718	X-RAY DIFFRACTION	99.73
4.69-43.48	0.1609	146	0.1393	11827	X-RAY DIFFRACTION	99.5

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	0.609483096842	0.0059268759873	-0.0405170660835	0.678529792557	0.561760667575	1.71699668927	-0.0225114523948	0.108132379424	0.0438721684061	-0.156281507285	-0.0338516903615	0.0885033296175	-0.274008792616	-0.121884328437	0.0390070280999	0.221957941279	0.00635492223133	-0.0103899240493	0.17989854729	0.0163926399996	0.178296393452	27.9790646944	29.835846424	12.3604891255
2	0.464490515845	0.0283727232338	-0.174634562656	0.523959594614	0.733215118531	1.42041158538	0.0104383301052	0.053187488922	-0.162148111247	0.0389362641361	-0.0946854242912	0.162228006226	0.245675689776	-0.387564951774	0.0400251164007	0.181143543627	-0.0371742287202	-0.00786774349115	0.228208485876	-0.01364959097	0.226158516345	21.0747286063	18.4949726238	22.2674684995
3	1.16239160025	-0.0238244419137	0.0952976310786	0.261288136675	0.247005303874	1.0009413152	-0.0466242376025	0.0577775336178	-0.0216467731553	-0.00907958917863	0.0382878395396	0.0587596329224	-0.141544585226	-0.00284538367273	0.0122599632546	0.163449230162	-0.00872526758557	0.00973743429393	0.11461049002	0.00950210599481	0.148835749833	32.9754405006	28.9162026396	25.6332366728
4	0.399202474328	0.0157823686589	0.101261808244	1.35989065859	-0.362882446031	0.704719265448	-0.0278811687918	-0.0537378150987	0.0488897536998	0.22698329897	0.0387781955528	0.113897857947	-0.101622128008	-0.167768225535	-0.0118191694352	0.20529506115	0.0283147262499	0.036479113671	0.199760260338	-0.00894573001551	0.171301810998	24.0562684335	21.1772166285	59.4638152734
5	0.550871640989	-0.347834381113	0.223505553575	2.0252787561	-0.976189072665	1.12370916578	0.00631854899156	0.0781029405256	0.0119663480801	-0.236521507872	0.0832219120759	0.138548060598	0.11618520671	-0.208546259164	-0.064357154848	0.173966358476	-0.00920997527541	-0.00592202422582	0.251717406698	0.00447284206431	0.198168189009	19.1321767972	10.9111026006	47.2330463646
6	0.977623789142	-0.120906046913	-0.0404524239432	0.785116241111	-0.0338951860622	0.452947857087	-0.0425550489423	0.0348815793888	-0.0440811297234	0.136844551522	0.0149976665837	0.026567058842	0.112179097871	-0.0944274572077	0.0242437956921	0.20987441198	0.00510366440458	0.011552777192	0.192869512342	0.0068763995701	0.160796735861	30.7779237307	8.58112216004	59.0395413587
7	0.41133750489	0.106504621249	-0.113949673662	1.83106755952	-0.359136301006	0.503885470735	0.0240482620731	0.0425510836336	-0.0213251636961	-0.152194143016	0.0396819725998	0.142781312569	0.0862307699075	-0.0607401477661	-0.0591347233717	0.207934618399	-0.0290332788861	-0.0113603519766	0.230141443266	-0.0501825951909	0.198213134635	28.6494244133	-13.895563131	5.17187649944
8	2.64385451583	0.125707108756	0.521214813085	3.46554000911	-0.560760199122	2.14720994349	0.066403949538	-0.122272299162	-0.000937265334073	0.212625269233	-0.0927916525996	0.438082781329	0.0290994420105	-0.28602726559	0.00456142477407	0.207217137465	-0.0498453743123	0.0194701623935	0.287625295865	-0.0228155817521	0.255364148696	19.8536823004	-18.992541446	16.4444944369
9	0.827089449642	-0.269448247543	-0.0129735600728	0.940832336528	-0.0870098523367	0.41477531123	0.0151406052036	0.0292367792176	-0.0206871438729	-0.177840014357	0.0176380614731	-0.0121583231703	0.00221724953823	-0.00133531384581	-0.0349655711231	0.202612653131	-0.0238559144536	0.0166319787304	0.229424757359	-0.0551610867572	0.172631811494	36.9028574763	-3.83069928158	4.60586126543
10	0.902898487999	0.276097170678	0.312605981801	0.606450916386	0.349065054132	1.57194095297	-0.0800026503788	-0.0158172253474	0.0194553883117	-0.0408516931171	0.0883106805282	-0.0958348738684	-0.284187931625	0.199596064084	0.00863596332732	0.181483434566	-0.0476822812678	0.000227451329699	0.189675480826	-0.0193670316849	0.185675596686	59.6170644455	35.2978801905	39.3166695109
11	0.624908262644	-0.0319575192729	-0.336115322643	0.365263344214	-0.499126770538	1.07944549158	-0.032180440718	-0.116335552145	-0.221240135168	0.0309968186757	0.0532130079426	-0.18653071555	0.184617669261	0.566007999185	-0.0309640743172	0.17852429159	0.00711369658489	-0.0232347883009	0.355253537315	-0.0136534268527	0.306309841312	67.6226976395	22.4864872891	39.2676607909
12	1.08895825777	0.126883655828	0.164773439602	0.390485512481	0.386690402312	0.720951056091	-0.0705213009842	0.0224776297018	-0.0188829162284	-0.119539963999	0.0833687197863	-0.118444847689	-0.155228061491	0.164238930563	-0.00740326618799	0.189959696195	-0.0393659118434	0.0177547929942	0.185249498321	-0.00704004106598	0.178439894615	53.3835183429	29.8296780577	27.579118443
13	0.348182644498	-0.0254728596346	-0.164378538644	0.307313018591	0.111334901663	1.11554203527	0.00405669138071	-0.0318271030941	-0.106215601307	0.0611595104945	0.021622907417	0.0867683802216	0.223302174437	-0.106975513016	-0.0274034715769	0.289642906372	-0.0369472776628	-0.0070896439625	0.161382551732	0.0349645401263	0.250787165775	25.6890101181	-25.9582077357	50.5518646175
14	0.52645189294	-0.423014258571	-0.436133999292	0.675006330845	0.875619549825	2.18162199081	0.0888059128229	0.0808059617648	0.0730713786756	-0.151011970919	-0.0471171040204	0.0814876329741	-0.269307117925	-0.212604501449	-0.064997326517	0.230024605961	-0.0104746505053	-0.00640143862756	0.182665566228	0.0327027944659	0.219282664023	20.00538071	-14.9024748991	39.5549496757
15	0.814401241725	-0.0891415581702	-0.160117307837	0.292487193196	0.0976815009304	0.911041593872	-0.0324813309158	0.0780725071466	-0.0556504796595	-0.011235180599	0.0515875146831	0.0566051281336	0.228999369591	-0.0562422110744	-0.0293123697014	0.293100095865	-0.0143668143481	-0.0218720280138	0.155305012495	0.0202392825009	0.234979609292	33.1047282138	-25.0300360433	38.1476411091
16	0.826436787185	-0.279684561786	0.266235074318	1.22615095083	0.0475715203255	1.37310596356	-0.0114633518895	-0.103361528286	-0.0517813379835	0.333540695117	-0.0187439549259	-0.20244750482	0.0902191414097	0.178429261162	0.0811760028266	0.298655129214	0.052833461615	-0.0840455369933	0.233082810254	0.0218808205056	0.273944878019	61.7046511028	-7.21053654019	67.6662942052
17	0.487073357641	-0.244138388627	0.140911765161	0.975098717576	-0.149697772139	0.0473908679079	0.00541216616605	-0.0781680777411	-0.0907227828418	0.236420189493	0.0709294358394	0.0679717318475	0.0311346899032	0.026827476463	-0.0805899119793	0.254938173293	0.0324671015192	-0.0404184077767	0.213802767086	0.0141598557273	0.224553580073	53.6313147165	2.24081055684	65.6499314177
18	0.820337210992	-0.318627122355	0.126626715558	1.09815070277	-0.162867397661	0.434995665339	0.0463529016513	0.0321830572001	-0.125802289972	0.102242962117	-0.0215410370799	-0.175943242151	0.0516022736753	0.149333511306	-0.0211942873959	0.203415154496	0.0295623442828	-0.0367917434155	0.231206586247	0.00319734737279	0.218730112556	56.9629179087	4.7469630773	58.5900578865
19	0.561891398813	0.276161036866	-0.046184730947	1.56445057113	0.449992534541	0.304431035427	-0.085561895502	0.0938847695367	-0.0422190491694	-0.378436367906	0.30104340363	-0.449992947172	-0.0996188712106	0.311849885709	-0.0940580828499	0.234236806409	-0.0940056031949	0.127574420617	0.416520370217	-0.161165948514	0.300222463847	63.8606730105	5.93128297421	3.98355562341
20	3.41973432794	0.299996773491	-0.58358245893	1.18305261103	0.138332479769	0.459422275759	-0.107206611502	-0.146988465523	-0.208745416991	-0.038384476125	0.228080978574	-0.305190068878	-0.0668847892199	0.375689449295	-0.016483774035	0.173584690761	-0.080732728285	0.0903836990283	0.534695910636	-0.229852472985	0.421388438677	70.2845253438	16.6042459063	14.4149947998
21	0.686993663645	0.286884608771	0.0407282013342	0.941653199959	0.0105241013366	0.360796838649	-0.124671262651	-0.12714986522	0.0273135501024	-0.0965585287124	0.237220461354	-0.231004920992	0.0990128417138	0.256088170956	-0.0666603731495	0.200557506359	-0.000686181938634	0.0531514446961	0.339914544353	-0.123143262622	0.252098294056	56.7774266258	-3.10096530929	6.72095064711
22	0.650395920116	0.282565263681	-0.375944964765	0.389876906628	0.0763839408125	1.24524199972	-0.0625737987726	0.178801321466	-0.288434824196	0.0202337783267	0.00220783251555	-0.213140204139	0.405460257937	0.140335246987	0.0650670984058	0.319640579922	0.1107852143	-0.00515946412682	0.277539589757	-0.0662917009249	0.403595456669	61.5015516659	-30.2057672795	29.3513699633
23	0.577916078141	0.0874414584629	-0.290090771788	0.466806371158	-0.146750850815	2.44310831982	0.0404444335707	0.133636253853	-0.0480832882713	0.023148541855	0.0869691108985	-0.185271364418	-0.0809674534645	0.33072743269	-0.159091449591	0.217451279134	0.0542253788737	-0.0295431439955	0.354987499111	-0.0472764189883	0.383688894658	68.8404901965	-17.0393708593	31.0559306223
24	0.718976064568	0.198613438269	-0.0493509301816	0.461029183084	0.151090109184	0.742695279174	-0.0385808037509	0.00477648858498	-0.143872163544	0.194003047039	0.048063678433	-0.238394777389	0.279956471163	0.184511932791	0.0304857063307	0.27434417035	0.0653877613123	-0.042128220803	0.159186473476	-0.00955305302982	0.272613997276	53.4441423678	-25.0153757471	40.0149595155

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:109)
2	X-RAY DIFFRACTION	2	(chain A and resid 110:148)
3	X-RAY DIFFRACTION	3	(chain A and resid 149:206)
4	X-RAY DIFFRACTION	4	(chain C and resid 2:109)
5	X-RAY DIFFRACTION	5	(chain C and resid 110:148)
6	X-RAY DIFFRACTION	6	(chain C and resid 149:206)
7	X-RAY DIFFRACTION	7	(chain E and resid 2:131)
8	X-RAY DIFFRACTION	8	(chain E and resid 132:151)
9	X-RAY DIFFRACTION	9	(chain E and resid 152:206)
10	X-RAY DIFFRACTION	10	(chain G and resid 2:113)
11	X-RAY DIFFRACTION	11	(chain G and resid 114:151)
12	X-RAY DIFFRACTION	12	(chain G and resid 152:206)
13	X-RAY DIFFRACTION	13	(chain I and resid 2:109)
14	X-RAY DIFFRACTION	14	(chain I and resid 110:148)
15	X-RAY DIFFRACTION	15	(chain I and resid 149:206)
16	X-RAY DIFFRACTION	16	(chain K and resid 2:61)
17	X-RAY DIFFRACTION	17	(chain K and resid 62:113)
18	X-RAY DIFFRACTION	18	(chain K and resid 114:206)
19	X-RAY DIFFRACTION	19	(chain M and resid 3:131)
20	X-RAY DIFFRACTION	20	(chain M and resid 132:148)
21	X-RAY DIFFRACTION	21	(chain M and resid 149:206)
22	X-RAY DIFFRACTION	22	(chain O and resid 3:113)
23	X-RAY DIFFRACTION	23	(chain O and resid 114:151)
24	X-RAY DIFFRACTION	24	(chain O and resid 152:206)

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