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- PDB-7tgm: Crystal structure of HSC-AMS bound DesD, the desferrioxamine synt... -

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Basic information

Entry
Database: PDB / ID: 7tgm
TitleCrystal structure of HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway
ComponentsDesferrioxamine synthetase DesD
KeywordsLIGASE/INHIBITOR / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme / LIGASE / inhibitor / LIGASE-INHIBITOR complex
Function / homologyChem-I3U / Chem-LMS / PHOSPHATE ION
Function and homology information
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136235 United States
National Science Foundation (NSF, United States)1654611 United States
CitationJournal: 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
DepositionJan 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Desferrioxamine synthetase DesD
B: Desferrioxamine synthetase DesD
C: Desferrioxamine synthetase DesD
E: Desferrioxamine synthetase DesD
D: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,175131
Polymers343,8085
Non-polymers13,368126
Water7,026390
1
A: Desferrioxamine synthetase DesD
B: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,29957
Polymers137,5232
Non-polymers5,77555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-315 kcal/mol
Surface area43030 Å2
MethodPISA
2
C: Desferrioxamine synthetase DesD
D: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,02254
Polymers137,5232
Non-polymers5,49952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-317 kcal/mol
Surface area42470 Å2
MethodPISA
3
E: Desferrioxamine synthetase DesD
hetero molecules

E: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,70940
Polymers137,5232
Non-polymers4,18638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9720 Å2
ΔGint-326 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.800, 237.400, 329.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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

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Components

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Protein , 1 types, 5 molecules ABCED

#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)

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Non-polymers , 7 types, 516 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-I3U / 4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic acid / N-(3-carboxypropanoyl)-N-hydroxycadaverine


Mass: 218.250 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-LMS / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE


Type: RNA linking / Mass: 346.320 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N6O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M Sodium phosphate pH 7.0 0.2M Ammonium sulfate 16% PEG 4000 (under oil)

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→49.6 Å / Num. obs: 169125 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 55.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.046 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 62652 / CC1/2: 0.5 / Rsym value: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TGK

7tgk


Resolution: 2.5→49.6 Å / SU ML: 0.3571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 1862 1.1 %
Rwork0.1888 167247 -
obs0.1892 169109 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23360 0 804 390 24554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007524627
X-RAY DIFFRACTIONf_angle_d0.904333473
X-RAY DIFFRACTIONf_chiral_restr0.05013628
X-RAY DIFFRACTIONf_plane_restr0.00784286
X-RAY DIFFRACTIONf_dihedral_angle_d8.24463474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.37351400.330212801X-RAY DIFFRACTION99.85
2.57-2.640.34351390.297712769X-RAY DIFFRACTION99.8
2.64-2.730.32551440.264712765X-RAY DIFFRACTION99.61
2.73-2.830.26211490.247112755X-RAY DIFFRACTION99.78
2.83-2.940.24031420.244112791X-RAY DIFFRACTION99.73
2.94-3.070.29691320.246912805X-RAY DIFFRACTION99.8
3.07-3.230.30571540.241812858X-RAY DIFFRACTION99.83
3.23-3.440.25041360.215312842X-RAY DIFFRACTION99.87
3.44-3.70.23061430.191512867X-RAY DIFFRACTION99.72
3.7-4.080.19931440.17412846X-RAY DIFFRACTION99.55
4.08-4.660.17581480.143912901X-RAY DIFFRACTION99.56
4.66-5.880.16931460.156212949X-RAY DIFFRACTION99.45
5.88-49.60.17881450.14913298X-RAY DIFFRACTION99.36
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.809570216803-0.0111575850847-0.2123184764920.6097807432710.4020946889350.184280344637-0.0390469943405-0.02489626353760.17069194921-0.01681292498590.0874578919357-0.0139977136951-0.0554766975537-0.0708932262611-2.92337209208E-60.4448951970370.0570028828472-0.075112129560.345742892308-0.03873110289530.38675404116168.170031424846.3412110069-63.7964225704
20.295381767897-0.1673272235480.06773730580210.796888897442-0.2924445473090.507464747431-0.0437061514234-0.1107519346560.02192344419770.0006813679705850.02092002102090.05076195409990.0271119356234-0.0313905841862-1.4491640882E-50.4144702559450.0759388480326-0.01215524586290.469574274062-0.01561514821710.33753611354.47885942423.2811609384-47.2394747893
30.7338142136740.43978066898-0.1343139587230.6924980177910.001067227681450.593575784510.00776319566635-0.2739351355940.2532905439690.1923011039890.009045710473480.126546939597-0.170070924508-0.0513637645419-5.88386909732E-60.6185641315020.18276142367-0.008852169318180.664864790063-0.168995710660.54125605556850.906142296849.248514161-40.7914304008
40.06365354677310.0005022607858640.0772251866274-0.01339799423080.07055595155790.1580761417130.121188915509-0.1097485401310.1610108019510.204275136505-0.0685227001476-0.0682708720841-0.07239925773840.211471804435-9.83647537702E-50.6696049255310.106763129465-0.07716412234640.608080402708-0.1696297073630.53186148308967.876936758847.7609918816-43.4897633776
51.32178610574-0.422496381834-0.0250788869960.361534853651-0.2066757632350.339508437529-0.121942302443-0.314458270463-0.1640536981160.08214127510920.0620745148715-0.03458867292980.07402178323440.0173883515253-0.0001748948139830.5137944244880.0884568620197-0.02449445102730.4866169394470.04728076112620.44468200609985.60330456842.66241327344-43.2130427813
60.701167947348-0.4107156372730.2615410003320.835273451828-0.4019251347770.0952151366329-0.02635119912980.0726128614018-0.0164759153387-0.05827537625130.00814690797058-0.0629578066470.0181770616465-0.02822179327836.10799300187E-60.4236155807050.0517899360711-0.009764907443970.341487162978-0.0269937753930.38513024318687.231907111915.0591165383-72.0523462732
70.802349765705-0.157283491377-0.03093907412240.278367705918-0.07324151899940.40595871538-0.0367283116766-0.1246848747110.0519851285781-0.0195335346967-0.00150229847455-0.191747220266-0.0422040006477-0.0345420287341-5.7498632789E-60.4599933721680.0758397894892-0.03082633087370.420472327926-0.02603937108520.605141013505109.0985415745.46838857349-59.6298812927
80.1241602947860.0800112987359-0.0002029061131230.0145084969206-0.03789172583110.10429398892-0.14002701065-0.2212608046090.3019457819440.1926729339520.234735115214-0.169683575782-0.02435080686540.0106091771426-8.01887957799E-50.5442783156720.0985643907722-0.1071080577690.620476121689-0.0574465201730.627369258656101.16713684114.9362245688-47.6006671368
90.6357182831450.04626934565170.1932371592960.975243988254-0.1545009429540.39028668930.03844147514910.0852644270986-0.217625700615-0.1120070183490.0617476756154-0.03433445190140.1773891068810.1402008681411.34849311154E-50.4961178560080.0881946775888-0.002444130470260.508371180885-0.1335826851420.551614697379105.50256094754.6071327102-67.0447241028
100.45550092668-0.1039986552980.2055649324780.9090204497430.2791373107310.550491198093-0.01838177259550.07018126170390.0281133367625-0.0001229629461730.0940009367364-0.166964231744-0.05450111844430.227770674868-7.51640449811E-50.3836641426360.0269199646193-0.002802780920030.64707503565-0.1186360426450.564989375353121.22539275179.1977488269-54.8491326165
110.6163928776830.179245532690.3160620475690.598868006026-0.1589218748560.515805941090.206873973752-0.0241255927759-0.2599762195650.2418467091860.0819045543048-0.3415081593580.2175668498360.25673820243-0.0001333279584770.5885162253530.184128620665-0.1613666093430.734101369964-0.1046771721990.804730007865126.18197295653.732363221-47.0396785839
120.2467043482560.269246030974-0.1748883339940.197281949686-0.170342996720.058353965970.178292438129-0.1555377254020.03796893636150.395474877621-0.094952306921-0.367973999677-0.00430870673983-0.06422653232590.0001639284195730.631108679920.0827374887861-0.1082983976290.599211116892-0.06095950487750.685558073294108.62120567555.7344804013-46.9920881496
130.5745267088770.007959486143720.118020475520.3511699180170.373917714160.9408152224030.128445668070.08413300247620.0822635741494-0.04387669055420.04346016389170.0598209375841-0.5193267991330.3085009649211.05573099966E-50.721569585204-0.1505889423750.1247960995840.575817110853-0.01782382672110.41500595057964.222504151825.0815438371-7.18578008842
140.1413069942530.0149231497096-0.002686211604770.845805949576-0.02639588020471.132056390920.133464952714-0.05530556053570.0292045444634-0.05294325502650.03702409989370.02435021394-0.08951081467820.0975446781438-1.34348105546E-50.484890184738-0.04054484498590.0306619275050.539279937143-0.007803826912530.4013406943754.23686582519.6417993728518.5869026971
150.2840668843970.295652905918-0.1690010523830.3542523616950.1661348528580.4453022548420.102911484138-0.07045902483860.128640645465-0.06610652755710.052642186956-0.144637226678-0.4297057190490.366684360199-5.85477119518E-50.795293672316-0.221361836130.1334086736970.760727771752-0.1331482689890.60691093726169.448283928132.20706781520.1412764389
161.99982801522.000163374082.000219905282.000016402642.000065701911.9999793089-2.84636104276-2.41141319009-3.020334664434.144898108550.0314292996332.86383775916-7.0651921407-2.341673061362.806140403411.319875778590.09281811855440.7067150131610.890384434558-0.25413508791.4371160655974.878882172947.472201096416.8227254526
170.84191775908-0.06179852375910.09556754738130.460181129967-0.03958078833950.4371926332160.0105096598099-0.1390970687390.1433805774960.07022394775090.00459557503306-0.013612417582-0.1039340667050.04799252061641.86620974219E-50.481810703326-0.00114997736665-0.004976154094560.458164293009-0.07280600448280.53411674781990.812658565999.9314928475-47.6068275321
180.733879845652-0.497838162815-0.307420088380.7099805529540.2455204084350.2947789417380.1133822366740.1788236348410.0109627899149-0.128239266671-0.07278041534860.04704862959-0.009733682136540.0574790679632-2.34771440423E-50.5029557489680.0438095586593-0.0516786541380.479984642094-0.03923359478960.49920508730384.909955141985.1535850488-74.6726644628
191.13760543932-0.1131168713450.06669019623630.2829116665420.1315125387470.5113891903150.0780112664561-0.0750827027321-0.0630259211503-0.0414323226607-0.01270345154690.233323576376-0.00824787806833-0.03753494202422.93048893686E-50.4502283999420.0594828586559-0.05804394805840.419477904233-0.002541675980310.66736176105865.148264812795.6991573689-59.9934709513
200.118242746570.0667242538777-0.1262479309320.0663234868144-0.09651021791880.3112781166410.03327291268510.106252536967-0.3619741858-0.0054906255822-0.114978636780.234907047731-0.0345463555774-0.0219907133517-1.73424794221E-50.4842912122650.05758763945290.008491071740290.544864526418-0.02263394303230.64642418674974.947990321287.3383054952-48.6484977525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 158 )AA0 - 1581 - 159
22chain 'A' and (resid 159 through 410 )AA159 - 410160 - 411
33chain 'A' and (resid 411 through 558 )AA411 - 558412 - 559
44chain 'A' and (resid 559 through 592 )AA559 - 592560 - 593
55chain 'B' and (resid 1 through 158 )BB1 - 1581 - 158
66chain 'B' and (resid 159 through 410 )BB159 - 410159 - 410
77chain 'B' and (resid 411 through 558 )BB411 - 558411 - 558
88chain 'B' and (resid 559 through 592 )BB559 - 592559 - 592
99chain 'C' and (resid 1 through 158 )CC1 - 1581 - 158
1010chain 'C' and (resid 159 through 410 )CC159 - 410159 - 410
1111chain 'C' and (resid 411 through 558 )CC411 - 558411 - 558
1212chain 'C' and (resid 559 through 592 )CC559 - 592559 - 592
1313chain 'E' and (resid 2 through 158 )DD2 - 1581 - 157
1414chain 'E' and (resid 159 through 410 )DD159 - 410158 - 409
1515chain 'E' and (resid 411 through 558 )DD411 - 558410 - 557
1616chain 'E' and (resid 592 through 592 )DD592591
1717chain 'D' and (resid 1 through 158 )EE1 - 1581 - 158
1818chain 'D' and (resid 159 through 410 )EE159 - 410159 - 410
1919chain 'D' and (resid 411 through 558 )EE411 - 558411 - 558
2020chain 'D' and (resid 559 through 592 )EE559 - 592559 - 592

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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