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- PDB-7tgl: Crystal structure of AMP+PPi bound DesD, the desferrioxamine synt... -

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Basic information

Entry
Database: PDB / ID: 7tgl
TitleCrystal structure of AMP+PPi bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway
ComponentsDesferrioxamine synthetase DesD
KeywordsLIGASE / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme
Function / homologyADENOSINE MONOPHOSPHATE / PYROPHOSPHATE
Function and homology information
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
D: Desferrioxamine synthetase DesD
E: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,73447
Polymers343,8085
Non-polymers4,92742
Water905
1
A: Desferrioxamine synthetase DesD
B: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,70021
Polymers137,5232
Non-polymers2,17719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-127 kcal/mol
Surface area42170 Å2
MethodPISA
2
C: Desferrioxamine synthetase DesD
hetero molecules

C: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,03914
Polymers137,5232
Non-polymers1,51612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7400 Å2
ΔGint-47 kcal/mol
Surface area43370 Å2
MethodPISA
3
D: Desferrioxamine synthetase DesD
E: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,51519
Polymers137,5232
Non-polymers1,99217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-110 kcal/mol
Surface area42660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.501, 236.745, 330.810
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 ABCDE

#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 , 6 types, 47 molecules

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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M Na PO4 pH 7.0, 0.2M Ammonium sulfate, 16% PEG 4000 (under oil 100%)

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.89→39.5 Å / Num. obs: 109861 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 80.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.06 / Net I/σ(I): 7.9
Reflection shellResolution: 2.89→2.94 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / Num. unique obs: 29609 / CC1/2: 0.6 / Rpim(I) all: 0.71

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Processing

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

7tgj


Resolution: 2.89→39.46 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1988 1.81 %
Rwork0.1894 107748 -
obs0.1903 109736 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.28 Å2
Refinement stepCycle: LAST / Resolution: 2.89→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23331 0 294 5 23630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924167
X-RAY DIFFRACTIONf_angle_d1.103732922
X-RAY DIFFRACTIONf_chiral_restr0.05513620
X-RAY DIFFRACTIONf_plane_restr0.00954271
X-RAY DIFFRACTIONf_dihedral_angle_d9.93313382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.47671310.39917245X-RAY DIFFRACTION94.66
2.97-3.050.32811350.31427706X-RAY DIFFRACTION99.96
3.05-3.140.31321490.26527645X-RAY DIFFRACTION99.95
3.14-3.240.28041360.24987693X-RAY DIFFRACTION99.91
3.24-3.350.31631480.24747695X-RAY DIFFRACTION99.86
3.35-3.490.30861390.25177634X-RAY DIFFRACTION99.92
3.49-3.650.26971370.22217708X-RAY DIFFRACTION99.48
3.65-3.840.25421490.20347738X-RAY DIFFRACTION99.87
3.84-4.080.2791480.18987701X-RAY DIFFRACTION99.86
4.08-4.390.20271370.17017696X-RAY DIFFRACTION99.99
4.39-4.830.18851410.14837695X-RAY DIFFRACTION98.95
4.83-5.530.18621490.16067788X-RAY DIFFRACTION99.86
5.53-6.960.23621430.17587811X-RAY DIFFRACTION99.59
6.96-39.460.18341460.1457993X-RAY DIFFRACTION98.98
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)
10.383362856443-0.00494182233811-0.6270421506320.348158128552-0.05630842630540.367043796794-0.06048646286440.001264183998080.20495432956-0.01491450395550.1015626288260.048729334458-0.131548350235-0.1196181911781.40962598735E-50.6560166431380.122215470757-0.1665502395250.46506980796-0.07427944427280.6084997752768.316480507546.1252934574-64.2602314696
20.412256808291-0.1021699265810.1386199747650.607533700083-0.09967896212080.420857476654-0.073747941042-0.1586886904040.04369868093770.01596124439690.009499124006310.01403587554980.0502673632724-0.1198477292141.20480745389E-50.5156850098550.157713668903-0.05475159761380.625481122896-0.04476969783330.41568340068954.565704664722.9636472529-47.4845057307
30.5282596606220.4410920518620.03579822402180.47505400129-0.2098239729090.315391569772-0.104885020738-0.3828433786360.364680437920.2648916055230.05616363865510.112568070938-0.209004593959-0.114159380738.91638584524E-50.8160370637690.316794774826-0.09486616651040.764354530276-0.2521849423580.67240080954454.004898698148.5425706081-41.7792907015
40.979967884579-0.236190271624-0.1323820284350.39088875611-0.1516868778080.221045020214-0.176841727318-0.341322185187-0.1406306547560.0406195155810.0542299158421-0.0915567478980.128374687426-0.054103832013-8.55310582456E-60.6286185349680.142322813278-0.03345463846430.6219252403640.02667992171330.55550141995685.68737550142.22472398655-42.8760354896
51.00678700489-0.135255819320.3319997186190.639026165454-0.5102937359-0.008787221803-0.122157832040.113506366546-0.001983207090210.004121937758510.0475276317651-0.08328710300650.0364534433678-0.0669678850115-5.03463197121E-60.6169267339370.0698063851983-0.008925915794750.432397955857-0.05467328349740.49684257314587.43179716114.4981106236-71.9537914275
60.6628234506980.06913956313880.02006209780610.166454542911-0.08051153784320.517153888159-0.0707578273977-0.1514735156670.07114315159730.005455554584910.0363029802548-0.178999566666-0.0114995914430.01732427000914.45096661751E-60.563709730660.12161590193-0.02056325470270.484136907223-0.02103313836950.709075296517107.8200989756.69429127018-57.1248822689
70.4151683163450.402184219537-0.03641306667750.3833811045330.1717487273360.4265145960380.164815990691-0.101406106167-0.164596535530.0666884612669-0.01913926741020.0893043166230.5299209031380.1779652197670.01025336320140.8429311587560.155925175994-0.1608259062410.7796187379280.008951242918710.54763878484964.0132133607-24.95257852317.14985105651
80.6239563426740.2165885035670.07808775649210.518902108245-0.07732290853580.9476166779560.2011747822950.170328849247-0.0461183711394-0.00420780882121-0.04889671376780.1425867854790.07808230026810.0748933470476-6.72961745874E-50.5454575022480.0779049598978-0.04735686199030.721220777504-0.02089745661680.47005468193554.1359084303-9.60311719988-18.5447781013
90.502873178183-0.139101268731-0.03606344698950.0567713294159-0.223211402530.6325352632510.2116591229180.221742498804-0.2681990556120.02113084148050.0168995303079-0.09421074119250.6750306023140.6143939923890.9998576271761.068286228580.371168675993-0.1644624228481.10742486972-0.1550972650360.75379500648670.7734324968-30.0071605927-18.2214998601
100.974208819684-0.06352110704520.06763594641240.4401614239910.04726364943050.214006133990.129396476635-0.2976173383120.2313020692530.0130393179968-0.0990361344469-0.102990885279-0.2778053675750.09875757463913.0006449922E-60.677922598904-0.03268870133940.03641676452640.682968382925-0.09607715107870.74827105444227.4690402876-18.9100032979-47.2988878911
111.24814376858-0.293195620198-0.4748969618370.498666132797-0.0984330142230.5203902570280.1114752326570.2135652365460.0241604000459-0.278221631367-0.06862487638530.0207878999935-0.07511154934130.0955610355445-2.52270980356E-50.6461042510640.114482943217-0.02373608065860.57232045142-0.0300178443970.60343935469221.4978799042-33.5376034911-74.6288384206
121.05790482168-0.106497169456-0.005996187381650.1899917544340.03307939961110.5798447998330.0669529705898-0.171150810317-0.0393041144095-0.0248537558179-0.01590872480050.152116710438-0.0573000123903-0.0147015307032-1.1649936956E-50.600794931560.103321845455-0.01607658871140.526242851099-0.005050155132860.7620074202523.56103796786-24.5356830592-57.5520440118
130.7617509567390.09013207603470.1469822006780.4567671838070.2621650028660.2890223642280.02556134155390.0583392574673-0.349425374914-0.0589576919197-0.0062939230566-0.1152947987320.1782261125930.1290808922490.0008428520371610.6658458559260.1882060992210.05458384975250.607894262378-0.1039562039240.76105432341942.2167549368-64.1861897176-67.4377453735
140.7173334049240.1987241372940.2505502181370.586113864348-0.2528355237010.09929648146920.0773727359912-0.0341733997477-0.00328715552992-0.09010510141930.0360343281122-0.1654084021-0.06919335174040.27232959214-6.07998988319E-60.528275457970.05030791567830.044345348110.969484385502-0.1521681795460.81823603543257.9337546769-39.6897437594-54.9211145634
150.1530307491080.718628467885-0.06067685891240.326486393438-0.09269166936810.1839568064310.0188145521416-0.170322915167-0.2363530048440.338030903690.0544406514067-0.3067307396580.291115000670.268564613532-0.0001217309901090.7805380845450.305308172729-0.1603637804181.02860426882-0.02249721983121.032988277859.8336070095-64.7504800996-47.2480662981
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 157)AA1 - 1571 - 157
22chain 'A' and (resid 158 through 410 )AA158 - 410158 - 410
33chain 'A' and (resid 411 through 590 )AA411 - 590411 - 590
44chain 'B' and (resid 1 through 157 )BF1 - 1571 - 157
55chain 'B' and (resid 158 through 410 )BF158 - 410158 - 410
66chain 'B' and (resid 411 through 592 )BF411 - 592411 - 592
77chain 'C' and (resid 1 through 157 )CN1 - 1571 - 157
88chain 'C' and (resid 158 through 410 )CN158 - 410158 - 410
99chain 'C' and (resid 411 through 591)CN411 - 591411 - 591
1010chain 'D' and (resid 2 through 158 )DS2 - 1581 - 157
1111chain 'D' and (resid 159 through 410 )DS159 - 410158 - 409
1212chain 'D' and (resid 411 through 592 )DS411 - 592410 - 591
1313chain 'E' and (resid 2 through 157 )EX2 - 1572 - 157
1414chain 'E' and (resid 158 through 410 )EX158 - 410158 - 410
1515chain 'E' and (resid 411 through 591 )EX411 - 591411 - 591

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