PDB-7d9e: Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens compl...

ID or keywords:

Entry

Database: PDB / ID: 7d9e

Title

Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with L-DON

Components

(Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03) x 2

Keywords

TRANSFERASE / theanine synthesis / transpeptidation /

enzyme /

protein engineering /

substrate specificity / reaction specificity

Function / homology

Function and homology information

hypoglycin A gamma-glutamyl transpeptidase activity /

glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process
Similarity search - Function

Biological species

Pseudomonas nitroreducens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Hibi, T. / Sano, C. / Itoh, T. / Wakayama, M.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Mutagenesis and structure-based analysis of the role of Tryptophan525 of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.
Authors: Sano, C. / Itoh, T. / Phumsombat, P. / Hayashi, J. / Wakayama, M. / Hibi, T.

History

Deposition	Oct 13, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 23, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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	7d9e.cif.gz	333.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7d9e.ent.gz	244.3 KB	Display	PDB format
PDBx/mmJSON format	7d9e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9e ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9e	HTTPS FTP

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Related structure data

Related structure data	7d9wC 7d9xC 5zjgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7d9w-2 2z8j-2 5zjg-1 6dd2-2 6j3i-2 5vpv-3 1wds-d 7d9w-1 2e5v-2 2xft-2 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: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03

B: Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	49.170, 99.160, 53.990
Angle α, β, γ (deg.)	90.000, 102.596, 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	Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 Mass: 40283.793 Da / Num. of mol.: 1 / Fragment: L-subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239KXH0
#2: Protein	Gamma-glutamyltransferase 1 Threonine peptidase. MEROPS family T03 Mass: 20825.461 Da / Num. of mol.: 1 / Fragment: S-subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas nitroreducens (bacteria) / Gene: SAMN05216209_3923 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A239KXH0
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-DON / 6-DIAZENYL-5-OXO-L-NORLEUCINE / (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID Type: L-peptide linking / Mass: 173.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₁N₃O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H₂O
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: 2.14 Å³/Da / Density % sol: 42.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The mother solution: 16% (w/v) PEG 8000, 15% (w/v) PEG 400, 0.1M HEPES pH7, 150mM Gly-Gly, 50 mM Lys The obtained crystal was soaked into the solution containing 50mM L-DON for 15 min before ...Details: The mother solution: 16% (w/v) PEG 8000, 15% (w/v) PEG 400, 0.1M HEPES pH7, 150mM Gly-Gly, 50 mM Lys The obtained crystal was soaked into the solution containing 50mM L-DON for 15 min before the X-ray diffraction measurement.

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.6 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The mother solution: 16% (w/v) PEG 8000, 15% (w/v) PEG 400, 0.1M HEPES pH7, 150mM Gly-Gly, 50 mM Lys The obtained crystal was soaked into the solution containing 50mM L-DON for 15 min before ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→46.53 Å / Num. obs: 80575 / % possible obs: 99.9 % / Redundancy: 2 % / B_iso Wilson estimate: 19.41 Å² / R_merge(I) obs: 0.059 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.5→1.52 Å / R_merge(I) obs: 0.588 / Num. unique obs: 6340

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.18.2_3874	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZJG

5zjg

Resolution: 1.5→40.1 Å / SU ML: 0.1358 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.3224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1567	4028	5 %
R_work	0.1419	76537	-
obs	0.1426	80565	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→40.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3908	0	21	321	4250

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	4060
X-RAY DIFFRACTION	f_angle_d	1.0185	5527
X-RAY DIFFRACTION	f_chiral_restr	0.0794	617
X-RAY DIFFRACTION	f_plane_restr	0.0065	728
X-RAY DIFFRACTION	f_dihedral_angle_d	14.386	1428

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 (%)
1.5-1.52	0.2648	135	0.233	2563	X-RAY DIFFRACTION	99.48
1.52-1.54	0.2436	141	0.2263	2678	X-RAY DIFFRACTION	100
1.54-1.56	0.1847	136	0.2063	2592	X-RAY DIFFRACTION	99.96
1.56-1.58	0.2228	140	0.1986	2664	X-RAY DIFFRACTION	100
1.58-1.6	0.2104	138	0.1834	2617	X-RAY DIFFRACTION	100
1.6-1.62	0.1953	138	0.1801	2627	X-RAY DIFFRACTION	100
1.62-1.64	0.2081	140	0.1723	2648	X-RAY DIFFRACTION	100
1.64-1.67	0.1854	137	0.1685	2605	X-RAY DIFFRACTION	99.96
1.67-1.7	0.1898	140	0.1629	2657	X-RAY DIFFRACTION	100
1.7-1.73	0.1805	138	0.1562	2618	X-RAY DIFFRACTION	100
1.73-1.76	0.1977	138	0.1546	2632	X-RAY DIFFRACTION	100
1.76-1.79	0.2007	140	0.1577	2666	X-RAY DIFFRACTION	100
1.79-1.83	0.1925	139	0.1542	2622	X-RAY DIFFRACTION	99.93
1.83-1.87	0.169	138	0.1512	2628	X-RAY DIFFRACTION	100
1.87-1.91	0.1542	140	0.1427	2664	X-RAY DIFFRACTION	100
1.91-1.96	0.157	137	0.136	2604	X-RAY DIFFRACTION	100
1.96-2.01	0.1373	140	0.1308	2653	X-RAY DIFFRACTION	100
2.01-2.07	0.1541	138	0.136	2636	X-RAY DIFFRACTION	100
2.07-2.14	0.1844	139	0.1374	2628	X-RAY DIFFRACTION	100
2.14-2.22	0.1288	139	0.1316	2654	X-RAY DIFFRACTION	100
2.22-2.3	0.1322	139	0.1261	2625	X-RAY DIFFRACTION	99.96
2.3-2.41	0.1371	139	0.1256	2652	X-RAY DIFFRACTION	100
2.41-2.54	0.1477	139	0.1314	2635	X-RAY DIFFRACTION	100
2.54-2.69	0.1499	139	0.1315	2651	X-RAY DIFFRACTION	100
2.69-2.9	0.1401	140	0.13	2654	X-RAY DIFFRACTION	100
2.9-3.19	0.1798	140	0.1308	2656	X-RAY DIFFRACTION	100
3.2-3.66	0.1536	139	0.1402	2640	X-RAY DIFFRACTION	100
3.66-4.61	0.1169	140	0.1219	2659	X-RAY DIFFRACTION	100
4.61-40.1	0.1692	142	0.1632	2709	X-RAY DIFFRACTION	99.93

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	2.88485472022	-2.09216643682	0.044744654669	2.47029948307	-0.273536266532	2.28044169514	-0.136772192373	-0.218991771319	0.613338906913	0.000278295101261	0.0199562557804	0.345572555079	-0.321021553249	-0.405355496871	0.0624283665931	0.210339456362	0.0729429036479	-0.0363913132988	0.204376119892	-0.0654251841642	0.344879991789	-15.2680924	8.38749601231	-5.93376505129
2	1.31306832489	0.405490448653	0.535306556184	1.03989170307	0.209127989996	1.42334726673	-0.0557063777509	0.216459549906	0.132993728024	-0.103603375254	0.0909916388804	-0.00337385980303	-0.0204793688846	-0.00979987322038	-0.0225187938834	0.121606057391	-0.00573869443157	0.000463146292278	0.159921155113	0.0351034849221	0.126395708524	-9.24241618833	-2.60022913664	-21.7749168492
3	1.83223055518	-1.40135447373	0.610491822438	4.08927116516	1.78145749812	2.97041435506	-0.0863660966379	0.0675381227181	0.0272222916797	0.0483089848738	0.157029334659	-0.246883359798	-0.0680157823717	0.304419921432	-0.0881133454194	0.128683623711	-0.0349523145136	0.0123126476732	0.216074312004	0.014150327773	0.247846085729	9.03551581374	0.303526260685	-13.4478574277
4	1.54630379141	0.928153255348	-0.334465822418	1.47864696831	-0.523674366587	1.94014734762	-0.110017585702	0.265109149545	0.136947503169	-0.179517872659	0.12250766756	0.0273839392323	-0.0623231906874	-0.0900088844749	-0.0300511326869	0.169647270218	0.0112989354523	-0.0179199175916	0.229359302687	0.0329838162968	0.172184042898	-10.9558172119	-2.5273769623	-25.4237485489
5	1.24273052221	0.415382309006	0.397338213788	1.27299496932	-0.545431509415	2.19671777197	0.113811749074	0.036133909756	-0.241129674445	-0.0102196936086	0.0662734964068	0.00859415515262	0.453542699489	-0.384482870297	-0.164500937101	0.264444027623	-0.0780213421846	-0.0350038857403	0.19313069207	0.000263842565661	0.197057901418	-17.6405542365	-28.2395203782	-8.86570793058
6	4.03662326942	0.225763056521	-1.62946762429	1.05560096186	0.0841412139951	2.96529939714	-0.0578331849969	0.0953905115886	0.128145310348	-0.0446263184304	0.0464313072279	0.0490126191937	-0.0955181681346	-0.0517478691298	0.0071217206711	0.112893184194	0.00452619970075	-0.0134588667003	0.109377742618	0.0212643534381	0.108679137793	-7.43781282831	-1.65446451972	-16.2228098876
7	6.19683250119	1.96503991894	1.93803963981	3.64246411219	-0.403289369375	5.31551181374	0.273551733564	-0.15370399875	-0.621528083731	0.431248332738	-0.132100586906	-0.361390814928	0.80827670518	0.0887540065743	-0.161006911487	0.323128461656	0.0175948042869	1.65809148504E-5	0.286457271951	-0.0316663472022	0.263173806977	-4.00442031536	-20.5416252775	-22.6112035707
8	0.935266589439	-0.25621246774	0.199778406303	1.57660638882	0.654986827286	2.2225640766	-0.064428832555	0.0940827350775	-0.0254604047949	-0.0365959552846	0.0101321602014	0.169651016262	0.0132739343794	-0.308827409277	0.0758865606806	0.12457919146	-0.0121661107827	0.00280955446881	0.188967673793	0.0194716911645	0.143124110025	-17.3873539221	-10.8841554755	-14.1241478609
9	2.33891704414	0.220055641155	0.56519123038	2.85168967088	0.517964998779	2.09860735203	0.118460484915	-0.0336775004244	-0.167147961776	0.0398068216049	0.0110582740952	-0.129457381793	0.172865615828	-0.162852573407	-0.107505754245	0.169573602207	-0.0281806139663	-0.00939501447697	0.123564901659	0.0114309039546	0.113895166316	-9.49803654373	-18.3986543687	-0.702427370045
10	4.21094160081	1.8137996128	2.95769958911	8.01453174295	6.89831051996	7.87100261341	-0.0288617961128	-0.162821981671	-0.34590147815	0.558168921279	0.156661754318	-0.347561001296	0.650203959137	-0.00451795203701	-0.0548018582395	0.425674093613	-0.0380926943157	-0.122772565779	0.138143625225	0.0418665711579	0.313476867402	-2.84493492675	-30.615639817	7.5714912984
11	2.42559557913	-2.0347221272	0.0073109618612	7.74601315724	-0.779059205478	1.39830897109	0.177789649488	0.104167270025	0.0399951810932	-0.174786605681	-0.126299854308	-0.896583640943	0.123534051316	0.0455622028423	-0.0519685994582	0.204261557878	0.00392895538792	-0.0198344440012	0.171748811304	-0.0311191472126	0.244464422279	-1.72309398704	-18.7732441375	-3.08804829317
12	3.34293602868	-3.84542576254	-2.50749477629	5.66237027443	2.05846131868	2.44322094894	-0.219423169134	-0.486798309684	0.209270090352	0.408189619047	0.0372501368949	0.315198740503	-0.137652807841	-0.538669075919	0.0571296098741	0.174230277823	0.0608241665724	0.0300275287228	0.362939625233	-0.0638148298712	0.194812268558	-19.3587597087	-1.29495058543	1.42593277184
13	6.41178184419	-2.75790045041	-1.26924842825	3.99181839287	-0.559118834338	2.57667613353	0.0388395349184	-0.284748086592	0.486298357779	0.149371952482	-0.158337398114	-0.0371850679177	-0.313591899492	-0.294508024684	0.114314385241	0.181093205675	0.0129078758755	-0.0304550066453	0.198054151641	-0.0813594073041	0.162071463709	-8.84455995898	0.780940056872	-0.246923187949

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 25 through 52 )	A	A	25 - 52	1 - 28
2	2	chain 'A' and (resid 53 through 159 )	A	A	53 - 159	29 - 136
3	3	chain 'A' and (resid 160 through 199 )	A	A	160 - 199	137 - 177
4	4	chain 'A' and (resid 200 through 270 )	A	A	200 - 270	178 - 248
5	5	chain 'A' and (resid 271 through 361 )	A	A	271 - 361	249 - 339
6	6	chain 'B' and (resid 364 through 401 )	B	D	364 - 401	1 - 39
7	7	chain 'B' and (resid 402 through 425 )	B	D	402 - 425	40 - 64
8	8	chain 'B' and (resid 426 through 456 )	B	D	426 - 456	65 - 95
9	9	chain 'B' and (resid 457 through 506 )	B	D	457 - 506	96 - 145
10	10	chain 'B' and (resid 507 through 516 )	B	D	507 - 516	146 - 155
11	11	chain 'B' and (resid 517 through 530 )	B	D	517 - 530	156 - 170
12	12	chain 'B' and (resid 531 through 544 )	B	D	531 - 544	171 - 184
13	13	chain 'B' and (resid 545 through 556 )	B	D	545 - 556	185 - 196

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