PDB-6tjl: Mature primitive pytochelatin synthase Alr0975 from Nostoc specie...

ID or keywords:

Entry

Database: PDB / ID: 6tjl

Title

Mature primitive pytochelatin synthase Alr0975 from Nostoc species bound to glutathione

Components

Alr0975 protein

Keywords

TRANSFERASE / glutathione / cyanobacteria / heavy metal / phytochelatin / protein-ligand complex

Function / homology

Function and homology information

glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding
Similarity search - Function

Biological species

Nostoc sp. PCC 7120 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Feiler, C.G. / Blankenfeldt, W.

Citation

Journal: To Be Published
Title: Mature primitive pytochelatin synthase Alr0975 from Nostoc species bound to glutathione
Authors: Feiler, C.G. / Blankenfeldt, W.

History

Deposition	Nov 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	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	6tjl.cif.gz	329 KB	Display	PDBx/mmCIF format
PDB format	pdb6tjl.ent.gz	224.7 KB	Display	PDB format
PDBx/mmJSON format	6tjl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6tjl_validation.pdf.gz	909.7 KB	Display	wwPDB validaton report
Full document	6tjl_full_validation.pdf.gz	915.7 KB	Display
Data in XML	6tjl_validation.xml.gz	20.3 KB	Display
Data in CIF	6tjl_validation.cif.gz	27.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjl ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjl	HTTPS FTP

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Related structure data

Related structure data	6th5S S: Starting model for refinement
Similar structure data	6th5-d 5ciy-d 3g7u-d 6kih-10 5m3x-1 6kih-12 4egr-3 2c7o-d 2iya-1 6kih-6 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	#212 - Aug 2017 Glutathione Transferases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Alr0975 protein

B: Alr0975 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.389, 47.832, 67.928
Angle α, β, γ (deg.)	90.000, 91.798, 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	Alr0975 protein / Primitive phytochelatin synthase Mass: 24627.822 Da / Num. of mol.: 2 / Mutation: C70S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0975, alr0975 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YY76
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.02 Å³/Da / Density % sol: 39.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.45 / Details: 15% PEG8000, 0.1 M MES pH 5.45, 0.2 M CaAc / PH range: 5-6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 11, 2012 / Details: lagittal bend Si crystal
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.87→46.25 Å / Num. obs: 32762 / % possible obs: 99.46 % / Redundancy: 3.3 % / B_iso Wilson estimate: 26.05 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.053 / R_rim(I) all: 0.099 / Net I/σ(I): 10.22
Reflection shell	Resolution: 1.87→1.937 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.841 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 3274 / CC_1/2: 0.621 / R_pim(I) all: 0.535 / R_rim(I) all: 0.999 / % possible all: 99.51

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TH5

6th5

Resolution: 1.87→46.25 Å / SU ML: 0.2626 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4735

	R_factor	Num. reflection	% reflection
R_free	0.2684	1638	5 %
R_work	0.2047	-	-
obs	0.2079	32749	99.33 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→46.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3448	0	44	118	3610

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0161	3634
X-RAY DIFFRACTION	f_angle_d	1.413	4937
X-RAY DIFFRACTION	f_chiral_restr	0.0639	555
X-RAY DIFFRACTION	f_plane_restr	0.0084	645
X-RAY DIFFRACTION	f_dihedral_angle_d	26.0091	503

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 (%)
1.87-1.92	0.3232	135	0.3105	2548	X-RAY DIFFRACTION	97.85
1.92-1.99	0.3494	135	0.2866	2570	X-RAY DIFFRACTION	99.82
1.99-2.06	0.3134	137	0.2665	2604	X-RAY DIFFRACTION	99.75
2.06-2.14	0.3044	135	0.2634	2562	X-RAY DIFFRACTION	99.7
2.14-2.24	0.3308	136	0.2387	2587	X-RAY DIFFRACTION	99.89
2.24-2.35	0.2931	137	0.228	2588	X-RAY DIFFRACTION	99.78
2.35-2.5	0.3062	136	0.2254	2601	X-RAY DIFFRACTION	99.67
2.5-2.69	0.2598	136	0.2238	2590	X-RAY DIFFRACTION	99.6
2.69-2.96	0.2799	136	0.2214	2594	X-RAY DIFFRACTION	99.56
2.97-3.39	0.2757	137	0.1987	2605	X-RAY DIFFRACTION	99.28
3.39-4.28	0.24	137	0.1609	2597	X-RAY DIFFRACTION	98.74
4.28-46.25	0.2192	141	0.1648	2665	X-RAY DIFFRACTION	98.42

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	0.293652833442	-0.115505559974	0.194670191802	0.775103469635	-0.271589715536	0.614386015045	0.00343258959743	0.154489364672	0.137843900844	0.103223928381	-0.0510181576767	-0.0631776595472	-0.177196388519	0.0544857948232	-0.0102140669739	0.458589508118	0.346540802961	0.00887086979888	0.713740223412	0.581519306108	0.161509207736	16.8722848688	12.7120169208	11.5727298654
2	2.5271714381	-0.6018512422	-0.273725166933	1.86195306291	-0.156507599112	1.24717194508	-0.178405794024	0.46857350481	0.0045758563908	-0.451235829914	0.163325381813	0.25623261836	0.0863948639776	-0.191819572626	-0.0487491275472	0.45224757802	0.112130820833	0.011087393446	0.777678392176	0.123768093779	0.259453610262	17.9197979136	1.64455843055	0.975043101543
3	2.81837519533	0.0994339133808	0.271787237573	0.913051738542	-0.317794339098	0.950114726795	0.11127529872	0.534367422333	0.0234954557616	0.00528429354619	-0.0274637578079	-0.0856180618473	-0.103910301016	0.00695644331042	-0.113178523708	0.213056359696	0.0557851075704	-0.0140088446978	0.171165398755	-0.00755674360626	0.203980981502	21.7735430708	-3.86465442885	19.7272812646
4	1.43924051937	0.911433148054	-0.384568434069	1.40006356734	-1.1169785958	1.0310415569	-0.193707740218	0.103731756261	-0.28758096072	0.3633024864	0.21110019921	-0.179581400389	0.0875467950428	-0.0624508080635	0.0434311233379	0.313846349267	0.0497866768997	-0.0168105135908	0.158227778273	-0.00110380126519	0.271644843974	19.6639507869	-14.9660184433	27.7428717026
5	1.86793481178	1.43047897953	0.102957921098	2.04777764172	0.648951485709	2.06942745369	0.147521136228	-0.0736106137359	-0.0536674146002	0.435090947543	0.0586327473748	-0.210466861883	-0.199952981648	0.208528191141	0.0229271872387	0.352636939013	-0.014210795756	-0.0411221992915	0.0714763484983	0.0244552199179	0.310032933917	31.0066653685	-8.63478788773	33.3671465008
6	0.996425811856	-0.0527200387921	0.268518303153	1.33735015952	0.414331079225	0.804463774152	0.109188643442	-0.0374340373069	0.0903329159612	0.675590194416	-0.212615450049	-0.124686492325	0.0230472907235	0.272901730223	0.0875332179163	0.293187887938	-0.0136599540123	0.0171492140239	0.16052136963	-0.0115899379976	0.301987851216	33.4423547836	-1.72172711404	29.3619537794
7	0.267854933469	0.0489469379209	0.527526038147	0.792873154238	-0.0535283830563	1.17974298335	0.120413576182	1.04032268267	-0.1751897365	-0.4042444688	-0.110935097795	-0.460574527282	-0.211691166409	0.332916714694	0.0509937080236	0.321725826938	0.074919956512	0.110052869253	0.762961546737	-0.026973723433	0.342847936203	37.4986007587	-1.44410934034	9.5339771552
8	1.43585515619	0.24001457548	0.321496959031	0.556614441981	-0.705570644627	1.4877124082	0.0959204852108	0.805283832931	0.206058215957	-0.0215064957391	-0.0311575858752	-0.0765937846383	-0.210832001251	0.0453191420611	-0.00117724984102	0.239319071985	0.0968846156745	0.0920804501408	0.365726055471	0.0666433799814	0.329663497877	29.727235974	2.7177665585	14.5274976625
9	0.535588664666	0.0935281519199	-0.0569014255074	0.386066964292	-0.394043138354	0.495084039878	0.116807482211	0.921928727329	0.653083573061	-0.184247866702	-0.0562014412862	-0.0215338290444	-0.189143636362	0.209768327027	0.0347872411152	0.302576419962	0.039233620982	0.0477771349155	0.484763067345	0.179746380373	0.333669590604	25.5375988991	7.30640084174	11.7652060555
10	2.62224016588	0.533287617417	0.138959709705	0.625338303295	-0.11702904069	2.40143882157	0.300453519907	0.434053528249	0.25707847715	-0.0457086776765	-0.339005336588	-0.259476214169	-0.276624979524	0.245569765481	-0.0202221978019	0.253780691568	0.00466706592656	0.0631098794482	0.254243102751	0.0744701690119	0.314575454059	37.9927398681	1.53268898203	19.7271069359
11	0.364013557332	-0.0595817161209	-0.0819536525432	0.962109170339	-0.112355673888	0.635384381962	-0.0715003691307	0.213048782354	-0.236692156573	0.187059085095	-0.101669190839	0.179489500978	0.374501360187	-0.0860206009673	-0.181835289688	0.470713888695	0.123689830133	-6.5755731098E-5	0.657727742422	-0.54874428227	0.524146656917	11.2582835275	-19.925739996	11.6212327817
12	1.02981324248	0.543173227708	-0.386556732678	0.827415267279	0.376299821803	1.01020533823	0.12885474839	0.833268110909	-0.0583906026044	-0.214065574169	-0.175825824882	0.101269983641	0.1593032646	0.00182687428819	-0.0236925861634	0.280299178671	0.115187128174	-0.0188026055519	0.463052538993	-0.0187043171304	0.225191476942	7.75058643627	-4.71389965508	14.4716247766
13	1.97830844467	0.729086853123	-0.278844449004	0.407293390354	0.278992078876	1.12769517884	-0.10197581242	0.343082864332	0.221872763641	0.206232762687	0.109123197722	0.0184552936828	-0.151048186598	0.104053284301	0.0434248306821	0.291869011436	0.0517462745587	0.0121083837014	0.140556372898	0.0278995391447	0.284390337502	7.43304927633	7.11750431888	28.9896109915
14	1.25262103639	0.147703973828	-0.134899200345	1.59058509118	-0.165239017454	1.09729251529	0.0492251080993	-0.0274711885694	0.0504987729459	0.494601960531	-0.0284197280317	0.147144598901	-0.0725256637049	-0.139717919523	0.0155843961439	0.286341369585	-0.00824456113337	-0.0215639165997	0.172292660558	-0.00473133893851	0.276069831698	-4.84753925165	-3.16726672054	30.8919801319
15	0.0750902474455	0.172287429683	-0.085795051095	0.569298695022	-0.241968620527	0.113031217894	0.126606828595	0.7342555716	-0.155462190026	-0.185385307967	0.0801069770324	0.380314256566	0.120844704982	-0.198864339373	0.132456421785	0.248686897813	0.0644042679835	-0.188142424966	1.07439399418	-0.0767022152289	0.291506119634	-9.06734286749	-5.66562646774	9.83853362227
16	2.53123373212	0.349346822365	-0.349119568622	1.29592889994	0.834325458628	1.58079448002	0.0695242439694	1.00932762106	-0.239506432779	-0.0129005858872	0.0147597914381	0.138046765794	0.138488083297	-0.0877371954271	-0.0410366834372	0.184983073355	0.073341081002	-0.052780234239	0.431516632697	-0.0822565407875	0.238127460816	-1.10147981667	-9.76073988417	14.6411085155
17	1.1866233897	-0.198661096017	-0.19385015131	1.0054892225	1.08978198997	1.76535428926	0.0550984806324	0.886271212965	-0.46652675996	-0.0888948373127	-0.0222350506921	0.0117629510723	0.163798118167	0.0555147115467	0.0535743509616	0.215219790724	0.0292698345252	-0.0538009388992	0.432847697091	-0.189618257351	0.280777806803	2.21066147654	-14.1660866825	15.1606776299
18	1.32899687475	0.203121517933	0.45701480857	0.165226610501	0.0298082855295	0.157741323364	0.0340961968646	1.49978750352	-0.367243665029	-0.445733874849	-0.208160648996	-0.0907560850864	-0.0028127552697	-0.407151924023	-0.144521166775	0.371758756581	0.0317605231565	-0.0757005788728	0.824740478901	-0.370312640112	0.295168340387	3.22714449722	-14.6137893205	11.0569817026
19	2.24419195176	0.177371935804	0.172538062225	2.14649238385	0.0962406172294	2.3881021686	0.1776428686	0.688592243572	-0.12082164988	-0.0547377125504	-0.304191084496	0.0410960221398	0.117040561159	-0.265436541943	0.0370691678169	0.177673011196	0.022887437704	-0.0286853575325	0.424497129398	-0.0678045810713	0.364632350231	-9.14356207984	-7.9816763356	19.574340086

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 51 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 52 through 81 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 82 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 114 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 135 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 136 through 161 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 162 through 176 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 177 through 221 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 222 through 241 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 38 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 39 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 106 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 107 through 135 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 136 through 161 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 162 through 176 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 177 through 191 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 192 through 221 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 222 through 241 )

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