PDB-7smg: Crystal structure of a (p)ppApp hydrolase from Bacteroides caccae

ID or keywords:

Entry

Database: PDB / ID: 7smg

Title

Crystal structure of a (p)ppApp hydrolase from Bacteroides caccae

Components

(p)ppApp hydrolase

Keywords

HYDROLASE / (p)ppApp hydrolase / Bacteroides caccae

Function / homology

Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / GTP pyrophosphokinase

Function and homology information

Biological species

Bacteroides caccae ATCC 43185 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Ahmad, S. / Alexei, A.G. / Tsang, K.K. / Trilesky, S. / Kim, Y. / Whitney, J.C.

Funding support

1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp.
Authors: Ahmad, S. / Gordon, I.J. / Tsang, K.K. / Alexei, A.G. / Sychantha, D. / Colautti, J. / Trilesky, S.L. / Kim, Y. / Wang, B. / Whitney, J.C.

History

Deposition	Oct 25, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 24, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7smg.cif.gz	306.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7smg.ent.gz	211.4 KB	Display	PDB format
PDBx/mmJSON format	7smg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7smg_validation.pdf.gz	707.2 KB	Display	wwPDB validaton report
Full document	7smg_full_validation.pdf.gz	708.4 KB	Display
Data in XML	7smg_validation.xml.gz	22.3 KB	Display
Data in CIF	7smg_validation.cif.gz	30.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sm/7smg ftp://data.pdbj.org/pub/pdb/validation_reports/sm/7smg	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: (p)ppApp hydrolase

B: (p)ppApp hydrolase

C: (p)ppApp hydrolase

D: (p)ppApp hydrolase

hetero molecules

71 kDa, 4 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)	144.136, 144.136, 63.485
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁
Space group name Hall	P6₁
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: -x,-y,z+1/2

#1: Protein	(p)ppApp hydrolase Mass: 17556.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides caccae ATCC 43185 (bacteria) Gene: BACCAC_01146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5ZE35
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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.: 106 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.99 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 8.5 Details: 0.8 M Lithium chloride, 0.1 M Tris:HCl pH 8.5, 32% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97859 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97859 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 33605 / % possible obs: 99.5 % / Redundancy: 14 % / B_iso Wilson estimate: 47.48 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.134 / Net I/σ(I): 24.8
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.39 / Mean I/σ(I) obs: 1 / Num. unique obs: 1567 / CC_1/2: 0.448 / % possible all: 92.7

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→47.64 Å / SU ML: 0.2834 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2345	1659	4.97 %
R_work	0.2014	31703	-
obs	0.203	33362	99.33 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4654	0	40	106	4800

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4920
X-RAY DIFFRACTION	f_angle_d	0.5027	6638
X-RAY DIFFRACTION	f_chiral_restr	0.0352	756
X-RAY DIFFRACTION	f_plane_restr	0.0027	863
X-RAY DIFFRACTION	f_dihedral_angle_d	17.2467	1904

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 (%)
2.3-2.37	0.3282	117	0.3031	2463	X-RAY DIFFRACTION	92.61
2.37-2.45	0.2884	124	0.2788	2634	X-RAY DIFFRACTION	99.6
2.45-2.53	0.2802	156	0.2779	2641	X-RAY DIFFRACTION	100
2.53-2.63	0.2855	130	0.2535	2638	X-RAY DIFFRACTION	99.93
2.63-2.75	0.2703	176	0.256	2607	X-RAY DIFFRACTION	99.96
2.75-2.9	0.2741	116	0.2313	2665	X-RAY DIFFRACTION	100
2.9-3.08	0.29	115	0.2467	2668	X-RAY DIFFRACTION	100
3.08-3.32	0.3129	133	0.2186	2666	X-RAY DIFFRACTION	100
3.32-3.65	0.2659	134	0.2035	2651	X-RAY DIFFRACTION	100
3.65-4.18	0.2079	172	0.1721	2641	X-RAY DIFFRACTION	100
4.18-5.27	0.1971	162	0.1549	2662	X-RAY DIFFRACTION	100
5.27-47.64	0.171	124	0.1762	2767	X-RAY DIFFRACTION	99.79

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	3.19629499402	3.06295363232	3.63068356385	5.77836547895	5.34638091476	5.32979295186	-0.773280257548	-0.600034245556	1.38548171533	-1.78547144569	0.631990735316	0.480521600852	-0.516065612388	0.894831171563	0.153032519806	0.615598560667	-0.0626654530928	-0.0210036082127	0.455974346353	-0.0937090868985	0.534912430532	32.97	51.495	-4.859
2	7.83871152821	0.645963614916	-0.161659786054	2.11743114986	0.576843936412	5.938113303	-0.0273482328911	0.755065663557	1.15151796019	-0.621783009871	0.273355160476	1.08354165546	-0.257468014252	0.699866120272	-0.130055347188	1.04199025891	0.095117780343	-0.0508000631122	0.827507424382	-0.0047520971043	0.577031002419	29.614	61.614	-3.671
3	8.40292013018	6.12372127883	-1.96157772057	9.39746855035	-1.01445887792	6.01902043486	-0.369926389055	-1.70170088712	0.53529994764	0.231864996878	0.50087769183	0.949745512219	0.0865375100012	-0.584905844185	0.169237038081	0.430388051367	0.0898747071255	0.0557488874793	0.782317855995	-0.123773506209	0.494652011917	22.99	47.466	3.196
4	9.01913102382	0.636919403724	-0.200687231737	5.13154187048	-0.223960984771	6.21621840804	0.0184950556991	-0.20316087672	-0.0787422245764	0.50481969011	0.0146307948106	-0.24842362566	0.105166771445	-0.0185110814265	0.00621440536419	0.366317241312	-0.0385974410347	-0.0505192368111	0.353641912516	-0.179225579547	0.453244808476	50.196	46.015	13.187
5	3.42741531697	1.80645114631	5.35892965877	6.71137176531	2.74557210596	9.59216813095	0.0600541547799	0.335927881296	-0.291186852004	-0.170520143173	0.0658645537987	-0.33127611862	-0.349730520857	0.0447881746677	-0.0913740213239	0.287946013919	-0.0386523322835	0.0713741691936	0.477895975663	-0.215972838416	0.586931336671	57.139	52.255	11.886
6	4.64058229666	-1.71339862818	2.49879457587	4.81637036178	-4.7989928959	4.97658881912	-0.751670743508	-0.807271147497	1.96159536729	0.825523801774	0.88443402348	-1.63566430921	-0.599903086453	0.0737370029688	-0.0553086051172	0.351723141604	-0.0716818750544	0.0521818052194	0.504432126522	-0.23892036826	0.70058730371	55.551	62.512	8.736
7	6.70989396303	3.35751332365	2.18565464862	6.70702786851	0.0393070553736	1.268530595	0.10259428423	-0.115989200509	0.221857932619	-0.132205405729	-0.117127074935	0.173727523307	-0.390615517857	-0.171508585812	0.000262643939342	0.517777819098	0.0471020726454	0.0610630974641	0.492029263813	-0.129085816487	0.339560521442	42.09	58.749	1.943
8	6.69371400636	-0.935945698515	-2.35651535298	4.53342352863	4.50916832324	4.94810945872	-0.0907616137728	0.402407080827	0.535782200685	-0.530576577718	0.159203648138	0.129670792766	0.334836391379	0.0464186821361	-0.00140904055075	0.458299903026	-0.001322018382	0.00747726581001	0.450083019559	0.0216070303378	0.339382689586	36.515	47.079	-25.987
9	4.80054887917	2.50038624088	1.93559931099	9.76908016556	-1.56933758692	5.15795949687	0.303527420004	-0.0262838879216	-0.0164437854752	-0.0221341392723	-0.475707524255	-0.0272188377033	0.797747441844	0.0723151949667	0.368422670285	0.446589278421	0.0718327960022	0.133425677216	0.400813564107	-0.00540134101701	0.280460985311	43.854	38.996	-17.906
10	2.63829015876	0.257189654659	1.77338645558	6.51531836174	-1.06923636149	8.11890558093	0.0671658204297	1.05209785767	0.270660627468	-1.33915189793	0.15258862867	-0.335291245683	0.0660819916854	0.161638241425	-0.161858422121	0.532487344565	0.0838742268361	0.216857779293	0.53456619667	0.0736389973987	0.479069246733	48.281	47.331	-29.722
11	1.83960401417	-0.796629665135	0.459531308712	2.74910066793	-2.16577753928	1.96937306827	-0.0379837325589	0.272533738021	0.164875325995	-0.559870290361	-0.109635240498	-0.731183735021	0.424544383669	0.182753011086	0.101294494295	0.420400771512	0.0686403232958	0.179994510723	0.403359318836	-0.0154107354374	0.474909756198	56.347	37.501	-17.396
12	6.13834090458	-4.61459226399	-0.926412180411	4.63128315468	0.304669961562	4.9226514348	-0.151450589369	-0.0318652443959	0.11720712121	-0.329315554044	-0.545515168586	-1.0832339291	0.0959958164901	0.625441391239	0.606758710735	0.40732734278	0.229931017696	0.195514865977	0.615575320303	0.125720648796	0.602897814918	61.193	33.949	-12.132
13	8.99761459071	1.70812367924	1.22337510862	4.65072366926	-2.52077544328	4.36104261589	0.0503912571962	-0.549554433423	0.423934567681	0.426203576204	0.261661572575	-0.264395283871	0.190233550005	0.182392882744	-0.294882976062	0.546249546558	0.0355679610374	-0.0362462660308	0.358710085912	-0.129381265879	0.377321578609	49.09	35.758	14.046
14	2.99801402124	-1.70935614387	-2.71267581846	3.65632999224	0.960030129555	8.70140553558	-0.0674202507397	-0.321055881263	-0.232347154955	0.400249020801	-0.051898809833	-0.0148467216156	0.643881701366	0.113025509787	0.126578567788	0.425866582369	-0.043155920783	-0.00135114725554	0.303342583153	-0.0342686213801	0.314725651821	45.57	23.971	8.169
15	6.02374662599	-1.50260888408	-0.351770110957	9.12123427442	0.477096864075	7.10825609757	-0.0132556185878	0.0773716824041	-0.299988810586	-1.02378991083	0.233809075598	0.67805452967	0.0604605654842	-0.324936239562	-0.131089832396	0.293309945026	-0.0232195450757	-0.00194563266532	0.48730862943	-0.0437959036394	0.257787574239	30.393	38.993	-20.878
16	6.95765942212	3.21041814396	1.77967760101	8.70862140025	-4.25246717164	5.83227948399	0.030179054371	-0.297523855692	-0.245530176975	-0.0253005007281	0.195230180826	0.00215508899677	0.463735424417	-0.196232846799	-0.217480283534	0.340553890478	0.0373213413296	0.0553158994941	0.379924490376	-0.0569581786795	0.366970601213	31.479	37.729	-11.586
17	3.76026344215	4.06188225911	5.23185018616	5.10312273079	6.22816499488	7.76690230378	-0.309681345119	-0.188460319244	1.27481862585	-1.11668346069	-0.694416267383	1.34145501876	-1.79460664528	-1.39589663441	1.2049194693	0.595222522916	-0.0195150549431	-0.114111533345	0.793644005989	0.162456442696	0.783034743938	20.031	41.64	-18.206
18	4.1364920678	-3.44596793527	3.37282295735	2.89948231979	-2.70589428764	7.80124573551	-0.182895099273	1.43134662106	-1.44795138108	-0.59079283289	0.636037387223	1.10753370333	1.56049106847	-2.47094618094	-0.418981067489	0.574661136456	-0.311121395154	-0.0134272996267	0.992109389209	-0.212090514439	0.735121004742	19.698	29.761	-22.424
19	6.82426001463	-0.641286831646	-2.56582790983	6.28929919353	-3.81051180746	3.69479315671	-0.421133962145	0.374387274694	-1.61362617785	0.244597601381	0.109573909637	2.26070680214	0.813394513171	-1.67135630582	-0.00348675448956	0.438523836697	-0.0919160989716	0.0797332639297	0.514625175184	0.00194236990739	0.748204159395	18.88	31.39	-11.831
20	4.44652802981	-4.4982331762	-6.25226680718	4.85398113813	6.55971628183	8.99335742586	0.0834805788766	1.63434333124	0.1347270429	-1.13193570891	-0.623697672118	2.66919926179	-0.557027800027	-3.16274984773	0.565435676476	0.577655007534	-0.0287074383431	-0.142693593916	1.16034639886	0.135660150156	0.964291937479	10.801	43.492	-8.391
21	5.76029649192	0.0179306384117	-2.28694359785	8.28222124898	1.3398511104	5.52844419604	-0.0715824127358	-0.934742629995	-0.903486069504	0.647613452292	-0.0698216008707	0.445693382409	0.620542816013	-0.789880302833	0.174395326301	0.357899538112	-0.0734393207487	0.0562404815328	0.648897628309	0.0768899161719	0.439733415268	21.349	38.638	-2.22

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN D AND RESID 114:119 )	D	114 - 119
2	X-RAY DIFFRACTION	2	( CHAIN D AND RESID 120:125 )	D	120 - 125
3	X-RAY DIFFRACTION	3	( CHAIN D AND RESID 126:144 )	D	126 - 144
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 4:40 )	A	4 - 40
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 41:72 )	A	41 - 72
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 73:89 )	A	73 - 89
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 90:143 )	A	90 - 143
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 2:18 )	B	2 - 18
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 19:51 )	B	19 - 51
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 52:81 )	B	52 - 81
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 82:124 )	B	82 - 124
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 125:145 )	B	125 - 145
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 1:40 )	C	1 - 40
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 41:144 )	C	41 - 144
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 3:29 )	D	3 - 29
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 30:52 )	D	30 - 52
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 53:62 )	D	53 - 62
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 63:72 )	D	63 - 72
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 73:82 )	D	73 - 82
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 83:89 )	D	83 - 89
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 90:113 )	D	90 - 113

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About Yorodumi

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Yorodumi