PDB-7tgj: Crystal structure of DesD, the desferrioxamine synthetase from th...

ID or keywords:

Entry

Database: PDB / ID: 7tgj

Title

Crystal structure of DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Components

Desferrioxamine synthetase DesD

Keywords

LIGASE / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme

Biological species

Streptomyces griseoflavus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Patel, K.D. / Gulick, A.M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM136235	United States
National Science Foundation (NSF, United States)	1654611	United States

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.
Authors: Yang, J. / Banas, V.S. / Patel, K.D. / Rivera, G.S.M. / Mydy, L.S. / Gulick, A.M. / Wencewicz, T.A.

History

Deposition	Jan 7, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
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	7tgj.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb7tgj.ent.gz	933.1 KB	Display	PDB format
PDBx/mmJSON format	7tgj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tgj_validation.pdf.gz	508.4 KB	Display	wwPDB validaton report
Full document	7tgj_full_validation.pdf.gz	537.2 KB	Display
Data in XML	7tgj_validation.xml.gz	95.7 KB	Display
Data in CIF	7tgj_validation.cif.gz	131.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgj ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgj	HTTPS FTP

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Related structure data

Related structure data	7tgkC 7tglC 7tgmC 7tgnC 5o7oS S: Starting model for refinement C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Desferrioxamine synthetase DesD

B: Desferrioxamine synthetase DesD

C: Desferrioxamine synthetase DesD

D: Desferrioxamine synthetase DesD

E: Desferrioxamine synthetase DesD

hetero molecules

348 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Desferrioxamine synthetase DesD

B: Desferrioxamine synthetase DesD

hetero molecules

defined by author&software
Evidence: gel filtration
139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Desferrioxamine synthetase DesD

D: Desferrioxamine synthetase DesD

hetero molecules

defined by author&software
Evidence: gel filtration
139 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Desferrioxamine synthetase DesD

hetero molecules

E: Desferrioxamine synthetase DesD

hetero molecules

defined by author&software
138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.099, 238.490, 327.889
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Desferrioxamine synthetase DesD Mass: 68761.516 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.56 Å³/Da / Density % sol: 65.42 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM Bis Tris Propane 300 mM ammonium sulfate 16% PEG 4000

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Data collection

Diffraction	Mean temperature: 113 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.85→96 Å / Num. obs: 111788 / % possible obs: 97.9 % / Redundancy: 9.9 % / B_iso Wilson estimate: 52.57 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.167 / R_pim(I) all: 0.056 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 9.2 % / R_merge(I) obs: 1.28 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 47251 / CC_1/2: 0.531 / R_pim(I) all: 0.426 / % possible all: 92.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5O7O

5o7o

Resolution: 2.85→81.97 Å / SU ML: 0.3292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2211	5403	4.84 %
R_work	0.1824	106291	-
obs	0.1842	111694	97.81 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→81.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22658	0	219	92	22969

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0095	23414
X-RAY DIFFRACTION	f_angle_d	1.0354	31911
X-RAY DIFFRACTION	f_chiral_restr	0.0532	3536
X-RAY DIFFRACTION	f_plane_restr	0.0091	4128
X-RAY DIFFRACTION	f_dihedral_angle_d	6.667	3248

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 (%)
2.85-2.88	0.3288	175	0.2876	3265	X-RAY DIFFRACTION	91.83
2.88-2.92	0.3095	158	0.2775	3335	X-RAY DIFFRACTION	92.53
2.92-2.95	0.2891	168	0.2688	3358	X-RAY DIFFRACTION	93.83
2.95-2.99	0.2888	162	0.2665	3389	X-RAY DIFFRACTION	93.28
2.99-3.03	0.3045	200	0.2606	3327	X-RAY DIFFRACTION	94.33
3.03-3.07	0.3305	164	0.2535	3419	X-RAY DIFFRACTION	95.01
3.07-3.11	0.2762	168	0.2425	3479	X-RAY DIFFRACTION	96.63
3.11-3.16	0.2556	172	0.2432	3437	X-RAY DIFFRACTION	95.81
3.16-3.21	0.28	160	0.2385	3504	X-RAY DIFFRACTION	96.29
3.21-3.26	0.2796	179	0.2298	3489	X-RAY DIFFRACTION	97.76
3.26-3.32	0.2789	185	0.2234	3541	X-RAY DIFFRACTION	98.08
3.32-3.38	0.2937	185	0.2161	3539	X-RAY DIFFRACTION	97.79
3.38-3.44	0.2719	171	0.2173	3529	X-RAY DIFFRACTION	98.27
3.44-3.51	0.2452	178	0.2074	3510	X-RAY DIFFRACTION	98.27
3.51-3.59	0.2362	182	0.2015	3575	X-RAY DIFFRACTION	98.79
3.59-3.67	0.2486	169	0.2057	3546	X-RAY DIFFRACTION	98.25
3.67-3.77	0.2497	197	0.1931	3581	X-RAY DIFFRACTION	99.29
3.77-3.87	0.2258	172	0.1873	3587	X-RAY DIFFRACTION	99.26
3.87-3.98	0.2604	180	0.1734	3606	X-RAY DIFFRACTION	99.34
3.98-4.11	0.1865	186	0.1549	3598	X-RAY DIFFRACTION	99.82
4.11-4.26	0.2	183	0.147	3621	X-RAY DIFFRACTION	99.87
4.26-4.43	0.1703	207	0.1436	3575	X-RAY DIFFRACTION	99.82
4.43-4.63	0.1831	207	0.1334	3635	X-RAY DIFFRACTION	99.92
4.63-4.87	0.1727	171	0.1345	3637	X-RAY DIFFRACTION	99.95
4.87-5.18	0.1705	204	0.1426	3633	X-RAY DIFFRACTION	99.9
5.18-5.58	0.2132	168	0.1642	3674	X-RAY DIFFRACTION	100
5.58-6.14	0.2187	188	0.172	3653	X-RAY DIFFRACTION	100
6.14-7.03	0.1877	179	0.1624	3685	X-RAY DIFFRACTION	100
7.03-8.85	0.1757	178	0.1533	3737	X-RAY DIFFRACTION	100

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	1.56929075368	0.389020911063	0.123840362908	0.743287908063	0.0861186672522	0.837446714571	-0.0894243498223	0.501944503798	0.237521689772	-0.258439889448	0.0833860132106	-0.142304742274	-0.0845967229147	0.0965611130649	0.0175980395995	0.371206368014	-0.0638872653969	0.0433924093383	0.377396718855	0.102318996048	0.351004677947	-40.103	-2.135	42.442
2	1.39948911429	0.271582309984	-0.07861736678	1.95363877045	-0.74180071656	0.741452576226	-0.0147562419622	-0.11984683086	0.0469277287578	0.148650136208	-0.119141826141	-0.262785730776	-0.0814861138027	0.0264098097779	0.119189062495	0.291330201668	-0.0582434530945	-0.00747046630137	0.251873685464	-0.00857693742554	0.247778113593	-39.253	-18.429	72.576
3	1.70858047156	-0.119108382402	-0.0505749373883	0.44785368263	-0.116318806787	0.932580122708	0.0315046732073	0.188493384768	-0.0320863905731	-0.00925536870853	-0.0664653771654	-0.26530674105	0.0925172810183	0.0454937361782	0.0748577478284	0.374724489984	-0.0701773967527	0.0275898602601	0.341230944443	0.0049897369122	0.641753982256	-17.582	-5.197	57.191
4	2.00422252818	-0.137144424481	0.490203343936	0.544082104168	0.182229655064	0.982712628874	-0.0208076083645	0.00426730463613	-0.30477849736	-0.0543604431483	0.114353894937	0.0220958014234	0.218992638798	-0.0241323347294	-0.0859085306836	0.35509189489	-0.0329668201985	0.0588944718895	0.268698931603	0.000116468478791	0.254583513471	-57.461	-46.476	63.368
5	0.931936780987	0.518493891851	0.24870549002	1.1765615345	-0.278741314785	0.778813695884	-0.0541446066584	0.147817596561	0.0440816407695	-0.0990705031231	0.0534099280271	0.0763397573151	-0.0174693390258	-0.14623216295	-0.00605061890143	0.336177656428	-0.025805404223	-0.0032501260198	0.419509211583	0.0415041659921	0.209629398522	-69.786	-19.987	45.533
6	1.0815088139	-0.670166410858	0.335757768805	1.27609582591	0.00875102733883	1.25457799718	0.0553658812657	0.335824750287	-0.203741656283	-0.34020059238	0.00829161214319	0.0447128634242	0.224214815196	-0.0552357689434	-0.107859952305	0.487971365116	-0.167084477332	-0.0393784395958	0.52323430413	-0.0940678909506	0.345910922475	-74.286	-48.95	43.352
7	2.31487954675	0.450837027555	0.253070307329	1.20981224774	-0.0405764528163	1.12539516806	-0.108648789062	0.576269557442	-0.141401034264	-0.209139804361	0.169631524288	0.0716633383093	0.144525815788	0.0476181803562	-0.0777557234042	0.362225435119	-0.0581451680738	-0.00526106419844	0.404743267304	-0.0415605253316	0.402861162986	-34.379	-100.653	47.145
8	1.62182885462	0.212749489743	0.195779677491	1.39977805151	0.250064235623	0.957451391035	0.0173830158312	-0.299003457434	-0.0509070466936	0.102656262213	-0.0534066461358	0.207453309797	-0.0318017925767	0.065210005554	0.0184272524257	0.336348402374	-0.0307470281412	0.0328992584014	0.308737936616	0.00887377390804	0.336555341228	-39.492	-82.376	75.379
9	2.40003216597	0.179387761403	-0.158423992592	0.418953271	0.311039788961	1.25389114566	-0.053092015787	0.218035860758	0.10968517611	-0.0366061957171	0.078653008533	0.272025050036	-0.0845700580822	-0.0168817296556	-0.031911640259	0.36696342786	-0.0797902542309	-0.0127596557966	0.312229565497	0.0888902528522	0.63074717435	-57.606	-98.089	58.57
10	1.31724672408	-0.582286279115	-0.250248998664	0.926077084964	-0.34320021139	0.555907205282	-0.00860092954186	-0.155840864005	0.358759255251	0.218599194907	0.0815424637371	-0.319394237945	-0.217952152406	0.169496154485	-0.0818856281582	0.347374996859	-0.0600772350135	-0.0783309450944	0.305964702439	-0.107075583616	0.436251476215	-20.173	-55.038	66.676
11	1.5861352715	0.276977614929	-0.517414499551	1.54684002588	0.402428256966	1.13114919968	-0.00239197090583	0.0616186766091	0.0175989824792	-0.0180241180622	0.0686745405265	-0.298792519763	-0.0159092377263	0.17649490897	-0.0436929107497	0.26212534824	-0.00101209273996	0.00404925709943	0.409195252961	-0.0320634580663	0.418034868183	-5.542	-82.489	52.841
12	0.810028322786	-0.693825403344	-0.182341866309	1.71661138749	0.207337658011	0.654977147713	0.135424641693	0.111848070657	0.328685006289	-0.302040297813	0.00470542866635	-0.531196910465	-0.284379498589	0.33236497958	-0.161803205418	0.42587479086	-0.136362781991	0.136970524926	0.511700569091	-0.00913958468516	0.706384199444	-0.721	-53.861	49.32
13	0.954010974486	0.154501636914	0.226562666494	1.13871775476	0.681840231448	1.30997551201	0.0397982416092	0.234348254685	0.216034899056	-0.201430494009	0.235975700508	-0.145829499368	-0.551617162806	0.218368720087	-0.231446935812	0.658125900944	-0.0426965811545	0.173803899903	0.478776167933	0.0425346271237	0.407528885196	0.804	-94.102	-7.598
14	0.618675187165	-0.116521504862	0.13216083541	1.80590375039	0.32644127405	1.7890221202	0.0694430541167	-0.0152473045742	0.0538177869049	0.0934505357265	0.174463943302	0.00198540396459	-0.0391504446132	-0.240061304523	-0.236553393131	0.337989023856	0.0385838888507	0.000969830228382	0.419202567479	0.092367203667	0.281891996351	-8.503	-112.958	19.247
15	1.21579053452	0.5746199232	-0.0780304276505	1.01224014069	-0.003759209374	1.62900047329	0.0714677171561	-0.0880221735305	0.190889767923	0.0108379992343	0.11816386513	-0.266756852707	-0.41331003782	0.237003431793	-0.177224603181	0.610972654963	-0.0464760982534	0.143496620987	0.457163028168	-0.0849795460329	0.454096191813	4.986	-86.855	16.917

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:158 )	A	2 - 158
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 159:380 )	A	159 - 380
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 401:591 )	A	401 - 591
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 1:158 )	B	1 - 158
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 159:380 )	B	159 - 380
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 381:591 )	B	381 - 591
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 1:158 )	C	1 - 158
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 159:380 )	C	159 - 380
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 381:592 )	C	381 - 592
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 1:158 )	D	1 - 158
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 159:380 )	D	159 - 380
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 381:591 )	D	381 - 591
13	X-RAY DIFFRACTION	13	( CHAIN E AND RESID 1:158 )	E	1 - 158
14	X-RAY DIFFRACTION	14	( CHAIN E AND RESID 159:380 )	E	159 - 380
15	X-RAY DIFFRACTION	15	( CHAIN E AND RESID 381:591 )	E	381 - 591

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