PDB-7u2s: Structure of Paenibacillus xerothermodurans Apyc1 in the apo state

ID or keywords:

Entry

Database: PDB / ID: 7u2s

Title

Structure of Paenibacillus xerothermodurans Apyc1 in the apo state

Components

Apyc1

Keywords

HYDROLASE / Anti-Pycsar / Nuclease / Immune evasion

Function / homology

Function and homology information

3'-tRNA processing endoribonuclease activity / metal ion binding
Similarity search - Function

Biological species

Paenibacillus xerothermodurans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Hobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Sorek, R. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2022
Title: Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity.
Authors: Hobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Leavitt, A. / Yirmiya, E. / Sorek, R. / Kranzusch, P.J.

History

Deposition	Feb 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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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Download

PDBx/mmCIF format	7u2s.cif.gz	266 KB	Display	PDBx/mmCIF format
PDB format	pdb7u2s.ent.gz	175.5 KB	Display	PDB format
PDBx/mmJSON format	7u2s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7u2s_validation.pdf.gz	429.5 KB	Display	wwPDB validaton report
Full document	7u2s_full_validation.pdf.gz	431.2 KB	Display
Data in XML	7u2s_validation.xml.gz	26.5 KB	Display
Data in CIF	7u2s_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u2/7u2s ftp://data.pdbj.org/pub/pdb/validation_reports/u2/7u2s	HTTPS FTP

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Related structure data

Related structure data	7t26C 7t27C 7t28C 7u2rSC S: Starting model for refinement 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
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Apyc1

B: Apyc1

hetero molecules

55.9 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)	60.030, 58.295, 76.188
Angle α, β, γ (deg.)	90.000, 101.900, 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	Apyc1 Mass: 27819.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus xerothermodurans (bacteria) Gene: CBW46_002070 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2W1NDJ7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.34 Å³/Da / Density % sol: 47.53 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES-KOH 7.5, 0.2 M Calcium Acetate, 10% PEG-8,000

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.55→38.64 Å / Num. obs: 74391 / % possible obs: 99.5 % / Redundancy: 4.2 % / B_iso Wilson estimate: 10.71 Å² / R_pim(I) all: 0.078 / Net I/σ(I): 5.4
Reflection shell	Resolution: 1.55→1.58 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3615 / R_pim(I) all: 0.297 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7U2R

7u2r

Resolution: 1.55→38.64 Å / SU ML: 0.1316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1929	2000	2.69 %
R_work	0.1727	72349	-
obs	0.1733	74349	99.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 15.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→38.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3872	0	4	690	4566

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	3962
X-RAY DIFFRACTION	f_angle_d	0.9265	5364
X-RAY DIFFRACTION	f_chiral_restr	0.0617	605
X-RAY DIFFRACTION	f_plane_restr	0.0064	688
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7126	1430

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 (%)
1.55-1.59	0.2239	140	0.2033	5044	X-RAY DIFFRACTION	98.13
1.59-1.63	0.2004	142	0.1879	5164	X-RAY DIFFRACTION	99.66
1.63-1.68	0.1986	143	0.1841	5143	X-RAY DIFFRACTION	99.53
1.68-1.73	0.2133	141	0.1815	5141	X-RAY DIFFRACTION	99.47
1.73-1.8	0.2426	142	0.1755	5121	X-RAY DIFFRACTION	99.32
1.8-1.87	0.2008	143	0.1793	5152	X-RAY DIFFRACTION	99.1
1.87-1.95	0.1968	141	0.1701	5122	X-RAY DIFFRACTION	98.72
1.95-2.06	0.1817	142	0.1593	5148	X-RAY DIFFRACTION	99.44
2.06-2.18	0.1821	144	0.1614	5193	X-RAY DIFFRACTION	99.93
2.18-2.35	0.1968	143	0.1674	5174	X-RAY DIFFRACTION	99.89
2.35-2.59	0.186	144	0.1741	5216	X-RAY DIFFRACTION	99.83
2.59-2.96	0.2026	144	0.1852	5203	X-RAY DIFFRACTION	99.78
2.96-3.73	0.1696	144	0.1671	5188	X-RAY DIFFRACTION	98.94
3.73-38.64	0.1916	147	0.1675	5340	X-RAY DIFFRACTION	99.87

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	2.03730012363	-0.098603646779	-0.361087676482	2.08225371307	0.337202327965	1.95253130514	-0.00456969461237	0.0119056908084	-0.0431366048844	0.305420493249	-0.068018259271	-0.220027092772	0.0537362699255	-0.196975983586	0.0419627704529	-0.0018850567826	-0.00979932679281	0.0411439821933	0.108434636783	-0.0236418589747	0.0222710342423	39.3656971858	4.86143775843	2.07127279878
2	0.99078185897	0.683796592509	0.162871544863	1.96451876961	0.441062459517	1.37265241917	-0.0237877816152	-0.153330479292	0.21098337339	0.0672720413333	-0.102348725589	0.144085084546	-0.163321066752	-0.23580363501	0.122062399818	0.0536019816733	0.0200053727282	-0.0124216532697	0.0679233583085	-0.019990222266	0.0761740815148	43.5602279884	14.0710441806	-0.474769545498
3	1.32570117229	0.123590606029	0.212736317597	1.30327734119	0.15111825102	1.37016475678	-0.0496910550724	-0.0750628755252	0.0966530124811	-0.000232866302702	-0.0367376865171	0.0809035320449	-0.121836348068	-0.134049595447	0.0760736526052	0.0569306021941	0.015746000189	-0.00645005502747	0.0707726764682	-0.0107022412874	0.0493775773276	41.0152569899	10.2864712361	-6.10414503869
4	1.13980516637	-0.297815586599	0.910811825781	1.71836483943	0.186042362793	1.56967736097	-0.0762130707457	0.0463037799402	0.22770141434	-0.160203394905	-0.234989736867	0.0680970222839	-0.427204703253	-0.162968974645	0.0846267179655	0.119002944656	0.035789442386	-0.0181817376255	0.0838491170899	0.00995017371349	0.0953587427571	40.1559544387	17.6653623815	-15.43085945
5	0.718902166245	-0.319585265814	0.460900912738	1.30503032341	0.400839910953	1.12020412715	-0.0550203147406	0.148181968465	0.0722752220028	-0.114916428315	-0.0188974020765	-0.13655908084	-0.147203143678	0.233778613359	0.0664952993983	0.0707757426624	-0.0234616924102	0.0182118875469	0.0864838111711	0.0388648966411	0.0724291036954	53.0617183268	12.4937428689	-15.8088707535
6	1.92721463821	-0.388795869017	-0.0846180956096	2.23607442047	0.132721527058	2.02087180133	-0.0287613819205	0.0129930296895	0.112251842432	-0.132729081021	-0.0339795515632	-0.0204992642089	-0.0727052638359	0.0420351179843	0.0877602954529	0.0629296562064	-0.0200947776529	-0.0264121001987	0.0676517989447	-0.0142189907052	0.0841643351787	56.2605200264	16.2587245144	2.78699687522
7	0.77796501401	-0.210298727136	0.0934193900076	1.39942396515	0.987597691761	1.62500342354	0.0454723896944	-0.0233109683402	0.0133148894972	0.0101130054026	-0.0795320454152	-0.153717940347	0.0241967816588	0.034757720053	0.00581256174866	0.0508661666916	-0.00444201915632	0.00692658860317	0.0544214920389	0.0102324193245	0.0846124602974	54.8354943432	4.85954920026	2.58708837786
8	0.755103726548	-0.00986079023211	-0.257850268844	1.12757110656	-0.0179554551712	0.936142724876	-0.205318766561	-0.335836528483	0.104602234005	0.237384016777	-0.00777531101899	-0.352053774174	-0.100208731096	0.301663767008	-0.548614630593	0.101608704987	-0.00974276499721	-0.0614872161677	0.164627998374	0.0011326484313	0.123970042933	56.8073562646	-0.426283092211	10.8858307929
9	2.70237713014	0.18199423027	-0.205987585053	1.82960740389	-0.200450167003	2.43019027702	-0.0904055878657	-0.0661834981593	-0.328183952456	0.239126198716	-0.0123544906477	-0.0979265386074	0.294140019963	-0.0357014113722	-0.0286089718433	0.0800106519082	-0.0054296665606	0.0160915563291	0.0597889560388	0.0216139187817	0.0820858818181	49.3746398014	-2.32245297556	8.31947832016
10	2.03567675178	0.206627230895	-0.470671374858	1.73078574009	-0.799919291117	1.63407386828	-0.0317737828203	-0.194607847144	-0.15461759876	0.166176540021	-0.0454835868324	-0.0140013221764	0.214863389693	-0.0600937019175	0.0250511339396	0.131363838932	-0.0308972857969	0.0345251990918	0.0806136068491	0.0135063835046	0.0645559590796	44.1599716232	-4.33052247782	12.0512524239
11	1.85920554188	-0.309233678052	0.00443711526396	2.66509558273	-0.718522211996	1.21447564022	-0.0402959422517	-0.239610561925	0.0135761963711	0.24580292926	0.0217063675151	-0.00313494459265	0.00707521172797	-0.205390037002	-0.00531510623812	0.0899428958773	-0.00708737645204	0.0229738063256	0.134845391189	-0.0166163439751	0.0517288973853	40.0197267954	4.541420455	13.2427638399
12	1.39554386819	-0.337452410459	-0.380199092172	1.56898384223	0.284580895814	1.27414072891	0.0314620147773	-0.126537973125	0.0244453575516	-0.0192380050537	-0.0974799837146	0.172171710789	0.0998910439449	-0.187161686168	0.0147910512051	0.0550312269713	-0.00948171010998	-0.00601154011129	0.0844613367849	-0.0151169854268	0.0451461787456	28.532876012	-3.56306464086	-20.6069523994
13	1.16439741681	0.250530573476	0.259315657161	2.03311815478	-0.0956913498129	1.45260997004	0.0586927267464	-0.113007664587	-0.0280683619819	-0.0155541662533	-0.0757551580598	0.0608692263969	0.0817845985521	-0.108670394185	-0.0304572145919	0.0443329748064	-0.0076507905295	-0.00840175158021	0.0673858270782	7.47538920961E-5	0.0362488527676	34.3685499702	-5.25363843107	-17.6798581855
14	0.667893055923	-0.0279548138188	0.513211243538	4.02911495226	-0.130594802021	1.86589688798	0.109678255142	-0.107834409652	-0.149998701207	-0.00723807560941	-0.138915243903	-0.00348795687433	0.32828959492	0.0661308490927	-0.0875593083874	0.105816078763	0.00279425926411	-0.00954141177711	0.0885647496719	0.0197884242556	0.0808530263395	42.2676485752	-12.5168775533	-12.5972914
15	0.919578919308	0.183497964277	0.896625182185	0.800121006563	0.114094669345	1.6236980834	0.0710307588567	0.132828949909	-0.0215254302788	-0.117038558411	-0.0317769030823	-0.10632719706	0.0955764070959	0.221553868056	-0.0230430060715	0.0639629312331	0.0305746611775	0.0220981642489	0.0801923803499	0.00322893067791	0.0611681213306	49.6269291403	-4.9916959524	-21.9770911739
16	2.16029833299	-0.122895859213	2.88179161733	1.83333168049	-0.414856752195	5.56086721261	0.00761639524581	0.352047037324	-0.0523853916611	-0.0899551919507	0.0648477141088	-0.0934640002219	0.0121618097609	0.530794581976	0.0092379354189	0.12829151144	0.0444648216017	0.0202669620816	0.0932330048734	-0.0186378688497	0.0898464549343	47.1768482596	-10.1741746876	-26.1950845976
17	0.475901722929	-0.111212440915	0.155940767657	1.93594206021	-0.518038603433	1.58558647583	0.0333095981812	0.136772048965	-0.00574860035782	-0.12850844083	-0.107428118562	-0.232461860996	0.142217892161	0.0179817900101	-0.229634883332	0.256554189629	-0.0407031860549	-0.059368461145	0.0704115509326	-0.045139200828	0.01116111684	33.8419773093	-11.0270404352	-35.3994063291
18	0.753369328955	0.455275503113	0.202834653588	1.12661512412	0.0633652446228	0.749509228049	0.00544945540272	0.0266080507109	-0.0371253441941	-0.216691665272	-0.0782281378015	-0.0403669751261	-0.00115120240693	-0.0871158928189	-0.0540558911508	0.126948081682	0.00319370329341	-0.00593116901577	0.0791069766814	-0.0114638103931	0.0625127446913	33.1364284172	0.364598783784	-33.8890444041
19	0.797869710093	-0.084378194121	0.0743434453576	0.51258269986	0.386465388031	0.39649719583	0.0800592417064	0.362736694755	0.0152317275418	-0.575447829791	-0.0387933893101	0.104695365353	0.249744191011	-0.230156366112	0.0929645532974	0.243848702848	-0.00448251431748	-0.0795220026881	0.203178483415	0.00475566772533	0.0732800606834	26.768768766	6.05104725379	-39.1156517354
20	1.98634505646	-0.373087568699	-0.797800732949	0.332070281453	-0.49329664068	2.11592281386	0.0912272447366	0.112195028359	0.222208563155	-0.296332960338	-0.0478280879976	0.161200446612	-0.207882370183	-0.154935209205	-0.0132177976384	0.131108264245	0.038411456703	-0.0381165006395	0.106960595832	0.00239129056504	0.113177563764	25.3791410486	6.94352885282	-32.3099308923
21	1.66890552182	-0.0695471104756	-0.0482502578956	1.22976219562	-0.547606268729	1.61285678768	0.0303625348932	0.137032105709	0.0968655408536	-0.152564138703	0.0309425781025	0.321401953996	-0.098412251276	-0.308536317436	0.028094686874	0.108529048442	0.0466674905702	-0.0520234832557	0.152514109322	-0.00911250450977	0.166594633941	19.419829731	9.25172832522	-29.0080229772
22	1.19600392722	0.134034212732	-0.122309002352	1.291702909	-0.317886969665	1.34773991944	0.0762670214225	-0.0142734241105	-0.00833477100264	-0.201268967847	0.125672180854	0.52293872704	0.095819348905	-0.511617206559	0.152164990187	0.0992664879923	-0.00330785143797	-0.0436866750882	0.219766168285	-0.0104274681563	0.19191109073	16.765328104	0.183117546161	-25.7348328367

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 1 through 21 )	A	A	1 - 21	1 - 21
2	2	chain 'A' and (resid 22 through 39 )	A	A	22 - 39	22 - 39
3	3	chain 'A' and (resid 40 through 69 )	A	A	40 - 69	40 - 69
4	4	chain 'A' and (resid 70 through 85 )	A	A	70 - 85	70 - 85
5	5	chain 'A' and (resid 86 through 129 )	A	A	86 - 129	86 - 129
6	6	chain 'A' and (resid 130 through 143 )	A	A	130 - 143	130 - 143
7	7	chain 'A' and (resid 144 through 163 )	A	A	144 - 163	144 - 163
8	8	chain 'A' and (resid 164 through 180 )	A	A	164 - 180	164 - 180
9	9	chain 'A' and (resid 181 through 201 )	A	A	181 - 201	181 - 201
10	10	chain 'A' and (resid 202 through 228 )	A	A	202 - 228	202 - 228
11	11	chain 'A' and (resid 229 through 248 )	A	A	229 - 248	229 - 248
12	12	chain 'B' and (resid 3 through 39 )	B	B	3 - 39	1 - 37
13	13	chain 'B' and (resid 40 through 69 )	B	B	40 - 69	38 - 67
14	14	chain 'B' and (resid 70 through 85 )	B	B	70 - 85	68 - 83
15	15	chain 'B' and (resid 86 through 111 )	B	B	86 - 111	84 - 109
16	16	chain 'B' and (resid 112 through 129 )	B	B	112 - 129	110 - 127
17	17	chain 'B' and (resid 130 through 143 )	B	B	130 - 143	128 - 141
18	18	chain 'B' and (resid 144 through 163 )	B	B	144 - 163	142 - 161
19	19	chain 'B' and (resid 164 through 179 )	B	B	164 - 179	162 - 177
20	20	chain 'B' and (resid 180 through 201 )	B	B	180 - 201	178 - 199
21	21	chain 'B' and (resid 202 through 228 )	B	B	202 - 228	200 - 226
22	22	chain 'B' and (resid 229 through 248 )	B	B	229 - 248	227 - 246

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