PDB-6uh4: B. theta Bile Salt Hydrolase with covalent inhibitor

ID or keywords:

Entry

Database: PDB / ID: 6uh4

Title

B. theta Bile Salt Hydrolase with covalent inhibitor

Components

Choloylglycine hydrolase

Keywords

Hydrolase/Hydrolase inhibitor / Bile Salt Hydrolase B. theta / Hydrolase-Hydrolase inhibitor complex

Function / homology

Function and homology information

choloylglycine hydrolase / choloylglycine hydrolase activity
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.51 Å

Authors

Seegar, T.C.M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5R35GM128618-02	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	5R35CA220340-03	United States

Citation

Journal: Nat.Chem.Biol. / Year: 2020
Title: Development of a covalent inhibitor of gut bacterial bile salt hydrolases.
Authors: Adhikari, A.A. / Seegar, T.C.M. / Ficarro, S.B. / McCurry, M.D. / Ramachandran, D. / Yao, L. / Chaudhari, S.N. / Ndousse-Fetter, S. / Banks, A.S. / Marto, J.A. / Blacklow, S.C. / Devlin, A.S.

History

Deposition	Sep 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2020	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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Mar 4, 2020	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 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uh4.cif.gz	599.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6uh4.ent.gz	448.3 KB	Display	PDB format
PDBx/mmJSON format	6uh4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6uh4_validation.pdf.gz	340.7 KB	Display	wwPDB validaton report
Full document	6uh4_full_validation.pdf.gz	342.8 KB	Display
Data in XML	6uh4_validation.xml.gz	2 KB	Display
Data in CIF	6uh4_validation.cif.gz	13.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uh/6uh4 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/6uh4	HTTPS FTP

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Related structure data

Related structure data	6ufySC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ufy-d 2w01-d 3mkm-d 3azt-d 2idj-d 4kg5-d 5ij8-1 3cl9-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Choloylglycine hydrolase

B: Choloylglycine hydrolase

C: Choloylglycine hydrolase

D: Choloylglycine hydrolase

hetero molecules

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

1

A: Choloylglycine hydrolase

B: Choloylglycine hydrolase

hetero molecules

A: Choloylglycine hydrolase

B: Choloylglycine hydrolase

hetero molecules

defined by author&software
Evidence: gel filtration
153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Choloylglycine hydrolase

D: Choloylglycine hydrolase

defined by author&software
152 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	3_554	-x+1/2,y+1/2,-z-1	1
crystal symmetry operation	4_454	x-1/2,-y+1/2,-z-1	1

Unit cell

Length a, b, c (Å)	98.580, 99.520, 162.120
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Choloylglycine hydrolase / Penicillin amidase Cysteine peptidase. MEROPS family C59 Mass: 37962.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: cbh_1, Btheta7330_00957, SAMN02910322_01222 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0ENF5, choloylglycine hydrolase
#2: Chemical	ChemComp-QC7 / (5R,6R)-6-[(1S,2R,4aS,4bS,7R,8aS,10R,10aS)-7,10-dihydroxy-1,2,4b-trimethyltetradecahydrophenanthren-2-yl]-5-methylheptan-2-one Mass: 392.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₄O₃ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	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: 2.72 Å³/Da / Density % sol: 54.8 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 21% PEG 3350 100 mM Sodium Citrate Tribasic Dihydrate pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.5→49.29 Å / Num. obs: 20034 / % possible obs: 97 % / Redundancy: 5 % / CC_1/2: 0.997 / Net I/σ(I): 7.84
Reflection shell	Resolution: 3.506→3.632 Å / Num. unique obs: 1916 / CC_1/2: 0.591

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6UFY

6ufy

Resolution: 3.51→49.29 Å / Cross valid method: FREE R-VALUE / σ(F): 3.12 / Phase error: 44.1373

	R_factor	Num. reflection	% reflection
R_free	0.2916	1877	9.37 %
R_work	0.2383	-	-
obs	0.2479	20033	97.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 187.45 Å²

Refinement step

Cycle: LAST / Resolution: 3.51→49.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10221	0	28	0	10249

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	10490
X-RAY DIFFRACTION	f_angle_d	0.4951	14224
X-RAY DIFFRACTION	f_chiral_restr	0.0416	1577
X-RAY DIFFRACTION	f_plane_restr	0.0032	1808
X-RAY DIFFRACTION	f_dihedral_angle_d	17.0101	3882

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 (%)
3.51-3.6	0.387	141	0.3614	1322	X-RAY DIFFRACTION	85.46
3.6-3.71	0.3418	144	0.3575	1407	X-RAY DIFFRACTION	89.79
3.71-3.83	0.3451	135	0.3164	1394	X-RAY DIFFRACTION	90.05
3.83-3.96	0.2921	142	0.3281	1402	X-RAY DIFFRACTION	89.13
3.96-4.12	0.3155	141	0.3238	1398	X-RAY DIFFRACTION	89.33
4.12-4.31	0.3581	142	0.2989	1387	X-RAY DIFFRACTION	88.74
4.31-4.54	0.2891	135	0.2844	1362	X-RAY DIFFRACTION	87.2
4.54-4.82	0.3069	142	0.2653	1386	X-RAY DIFFRACTION	88
4.82-5.19	0.2777	142	0.2441	1425	X-RAY DIFFRACTION	89.68
5.19-5.71	0.3178	139	0.2583	1404	X-RAY DIFFRACTION	88.8
5.71-6.54	0.3134	141	0.2467	1416	X-RAY DIFFRACTION	87.52
6.54-8.23	0.274	146	0.2128	1409	X-RAY DIFFRACTION	86.34
8.23-47.57	0.2554	150	0.1682	1477	X-RAY DIFFRACTION	86.48

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	1.44298639176	-0.975807635388	0.313733570491	4.17694454196	0.886243691812	1.20609000586	-0.364361294387	-0.132543947291	-0.525260977988	0.00336350496367	0.784229824356	-0.548866962571	0.266524634982	1.32670920281	-0.194710939209	2.33450720708	0.0612369665162	0.586514873745	1.99441953638	-0.17458873571	0.931074559535	34.8510861523	11.0704447201	-15.5881952366
2	1.36741793556	-0.978071257527	0.516758190586	3.29308779492	0.670032140897	0.477337313488	0.254007606528	0.295508057448	0.272335099362	0.937840213733	0.323500645573	-0.886266890348	1.29661570839	-0.556332082457	0.231315074709	3.37135494205	0.414131716887	-0.0371575239736	4.35583016715	0.459268663212	1.06183633953	15.0638787402	27.5756059588	-55.2743037449
3	0.50115711294	0.214340857163	0.146315755613	1.82108416525	0.424331610508	0.119539615254	-0.0431287158372	0.0833576861337	0.339293652681	-0.135179931162	0.694642033247	0.106179454229	-0.384922025414	-0.263090422185	0.741178755796	3.64315475759	0.0420568952507	0.835750392813	3.55560309709	0.487333972472	1.21974728399	8.30330496714	33.7073907945	-49.6146664789
4	2.11230138766	0.0639563898676	0.509593898947	1.48338924811	0.958565246198	0.765095851299	0.767191298454	-0.423074243903	-0.832248880201	0.365080567021	-0.939610422224	-0.139644496361	-0.0213697387459	0.858741063282	0.0715779731192	2.16206189725	0.757000358964	0.217159412379	4.34287655912	0.487748943748	1.18790587251	3.08630584269	37.1637065406	-70.8596094557
5	0.303856186094	0.0560949105225	0.385219253077	2.05635671442	1.24800955525	1.28361616474	0.353661565701	0.0111616411612	-0.416627772921	-0.441709879036	0.399398061759	-0.840630350471	0.356907139447	0.917316586385	1.07290492395	2.63963328351	0.156811809821	0.144841881256	4.87927027876	0.827359866396	1.08028109579	17.0955829505	17.6644452861	-64.8340423792
6	4.13408006558	1.87368802329	0.684933040277	1.8653523003	-0.102625811218	0.357597580136	0.0657943482527	1.52104757533	0.338466957549	0.355731931483	0.590461796195	-0.0132909622498	-0.538041206919	1.06599845825	0.164762428129	2.04760570565	-0.626198731371	-0.0931939127382	3.97570358429	0.171627811998	1.10135216934	53.2767088135	26.0577572017	-59.2595645246
7	3.44109762136	-0.928195079562	0.591650246218	0.999311255017	-0.12952134188	0.106781879188	-0.108712914531	1.59878700734	0.139020070913	0.611785574696	-0.548962455448	-0.628084251425	0.371066921921	1.13745125041	0.466954194949	2.91371348869	-1.36159662099	-0.481641004034	3.45627654857	0.536395601015	1.38987611915	52.5699402192	21.8721199582	-51.9592036108
8	1.04312554106	0.565043438434	-0.376282080048	0.813060593199	0.164131312464	2.62136334332	0.313355480555	1.7033700814	0.241041803854	0.711140605961	0.407077584549	0.0798446413289	0.560463668541	0.466061413731	0.415075494546	2.40627956851	-0.803229402533	-0.198793774033	4.31085488808	0.146547242413	1.10844308845	57.580629299	10.3675761328	-68.7265583901
9	0.33330188642	-0.893174783028	-0.666186424986	2.69026485159	1.47408422439	1.74320290964	-0.0406820467083	-2.17487233482	0.373117784838	0.72067455064	0.871977164493	-0.783234138208	-0.228601910047	0.153863121404	2.18789964233	2.56033587493	0.0439778139244	-0.795373687625	5.36450454816	0.446150717108	0.92670376205	52.5523350011	23.8253178208	-75.0702161722
10	0.656464530747	-1.68198767938	-1.31831438112	4.61727700309	3.55714795193	2.8975226133	1.95964522317	0.526030401742	0.5479219949	-1.80275957678	0.259536909514	-1.11669518091	-0.934628669135	2.17274037163	0.699885182656	1.88793304573	0.502318915351	-0.451766882991	3.96247841014	0.049075778625	1.44404071821	57.5036448098	38.2054351862	-66.5941429446
11	3.94442012115	-0.584249163145	-1.17328285591	3.12679249212	1.05365080135	0.615367991878	0.43839547514	-0.361707350209	0.0568128281948	-0.456835004595	-0.125964023855	-0.064556687403	-0.626595494528	0.801445356318	-0.347542214586	1.79564175917	0.0877352430723	0.0857756914219	1.39588583935	0.0409507980268	0.623329101629	21.5522236598	15.2273072749	24.3855599053
12	7.70623280457	1.75011268128	-0.180376589124	4.80310552315	2.93172205507	2.68814449372	0.617751593545	-1.28085615212	0.944343102138	-0.570247788613	-0.61103515203	1.90678482258	-3.09290400034	-0.995618775759	0.0623596783547	2.73759295384	-0.229873608879	0.103687454212	1.43914089074	-0.474062867641	1.37792371439	9.28703754884	22.3871313785	27.414847785
13	5.36912454753	2.3608742516	1.89697070111	4.39822628067	1.23271141925	1.18218057255	0.515164761198	-0.374042529965	0.0382401758916	0.0945843660346	-0.0796655501847	0.0545826052186	0.035221351099	0.464495641884	-0.438636161658	1.62036361227	-0.0295428320288	0.133262943516	1.11638460403	-0.0414192702427	0.470184189713	18.8877039866	7.97953284291	11.9844932414
14	1.97232720133	-1.53924384754	0.80009702273	5.14784536621	-2.05645244699	5.48177483623	-0.918553171365	0.765246301703	0.340473759346	0.676870018033	0.718200546788	-0.11095382813	-0.896391763409	2.17465702132	0.149828076385	2.15681779361	-0.706855649673	0.281150460423	1.68759787857	-0.39099824648	1.13385727341	27.9990775911	27.0932811923	16.9812063271
15	3.12925191065	0.723066950857	1.08376985692	0.478346366462	0.527400097745	3.84364581882	-0.214791937484	0.419273387942	-0.1373793043	-0.807496478347	-0.660794802203	0.105073472005	-0.652951815956	1.06990410695	0.627642228187	2.65136913017	0.466009880483	0.400602850572	1.816942968	-0.143293095803	0.836158705794	27.555047754	7.62355276864	-23.1963406387
16	5.76654747007	-0.657294234716	1.91262038356	2.7518424419	-2.53088635263	2.76496411086	0.600462636762	1.53160666317	-1.15773459927	-0.724804903099	-0.254645574599	0.275893700899	-0.601880782321	0.723569539161	-0.34476012974	1.95898328292	0.55784133956	0.187934964498	1.77281401114	-0.110853086392	0.814479275789	22.8645332541	3.24803250395	-27.9729901485
17	7.71624245593	-2.83812317772	-2.01608990123	1.04897829882	0.482429009213	7.40007268041	-0.169670353072	1.12733959322	0.405586221663	1.22630388759	0.134034380311	-1.70015626509	3.12251284267	-0.172658354291	-0.241864392299	3.36934191498	0.839038987202	0.150077722251	1.31772774503	0.2071472299	1.39914185383	11.802426814	3.33161440831	-29.3955515344
18	9.26882184379	1.7568479211	1.8015876848	5.8672636808	6.11351694866	7.63461890372	-0.134294435965	0.369236712206	0.0552115656826	-0.990917990614	0.315842930789	-0.0932141684344	1.26646765636	-0.888550582462	-0.296803810955	1.64350194671	-0.104718511569	0.179592142552	0.95193682396	0.247339181987	0.84137412939	6.91088404421	8.19689490573	-11.5577076732
19	9.29788376727	-0.092793850493	1.4999384998	0.264205488318	-0.780243694421	8.01601311433	1.0784087018	-0.917279541107	0.134443723203	-1.39302449405	-0.320597829327	-0.578782195593	0.265978459643	0.467939766294	-0.751415652801	2.18471233136	0.400366004319	0.306383311871	0.994516066154	-0.0446442480624	1.27118417887	19.9889931285	4.13993528561	-3.86088707217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 254 through 326 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 1 through 109 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 110 through 166 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 167 through 253 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 254 through 326 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 1 through 94 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 95 through 146 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 147 through 238 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 239 through 272 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 273 through 326 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 121 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 122 through 140 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 141 through 302 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 303 through 329 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1 through 55 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 56 through 151 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 152 through 167 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 168 through 223 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 224 through 253 )

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About Yorodumi

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Yorodumi