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

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Basic information

Entry
Database: PDB / ID: 7tgn
TitleCrystal structure of DesD, the desferrioxamine synthetase from the Streptomyces violaceus salmycin biosynthetic pathway
ComponentsDesferrioxamine synthetase DesD
KeywordsLIGASE / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme
Function / homologyCITRATE ANION
Function and homology information
Biological speciesStreptomyces violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,94730
Polymers274,2824
Non-polymers1,66526
Water4,486249
1
A: Desferrioxamine synthetase DesD
B: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,91313
Polymers137,1412
Non-polymers77211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-10 kcal/mol
Surface area42750 Å2
MethodPISA
2
C: Desferrioxamine synthetase DesD
D: Desferrioxamine synthetase DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,03417
Polymers137,1412
Non-polymers89315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-9 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.530, 108.530, 517.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11D-715-

HOH

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Components

#1: Protein
Desferrioxamine synthetase DesD


Mass: 68570.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces violaceus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 90-100 mM Potassium citrate 25% PEG 8000 50 mM MES

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.3→49.47 Å / Num. obs: 138685 / % possible obs: 100 % / Redundancy: 28 % / Biso Wilson estimate: 56.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.032 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10146 / CC1/2: 0.65 / Rpim(I) all: 0.519 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.47 Å / SU ML: 0.3033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 2000 1.44 %
Rwork0.1961 136670 -
obs0.1966 138670 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17615 0 107 249 17971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008818155
X-RAY DIFFRACTIONf_angle_d0.9924728
X-RAY DIFFRACTIONf_chiral_restr0.05382773
X-RAY DIFFRACTIONf_plane_restr0.00963205
X-RAY DIFFRACTIONf_dihedral_angle_d6.24732543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.33481410.28949649X-RAY DIFFRACTION99.99
2.36-2.420.3411400.27369569X-RAY DIFFRACTION100
2.42-2.490.31721400.26399602X-RAY DIFFRACTION100
2.49-2.570.31331410.26439635X-RAY DIFFRACTION100
2.57-2.660.29041420.2429627X-RAY DIFFRACTION100
2.66-2.770.26691410.22799664X-RAY DIFFRACTION99.99
2.77-2.90.28341410.22739661X-RAY DIFFRACTION100
2.9-3.050.28231420.23099675X-RAY DIFFRACTION99.98
3.05-3.240.25931430.2289721X-RAY DIFFRACTION99.99
3.24-3.490.22681420.2099784X-RAY DIFFRACTION99.99
3.49-3.840.23121430.19899784X-RAY DIFFRACTION99.98
3.84-4.40.23431450.16899858X-RAY DIFFRACTION100
4.4-5.540.20281450.16419972X-RAY DIFFRACTION100
5.54-49.470.17151540.172610469X-RAY DIFFRACTION99.92
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)
11.26987576531-0.389020305147-0.08788192929291.487194135780.2132805959331.76459703154-0.139033402196-0.2846857397120.1549327300580.3864112419770.168633954323-0.255776720281-0.1388565611920.121937683964-0.01949723540080.8366341074210.0776825982906-0.004762751829770.509596418288-0.03562613538840.578365784975-40.227203408720.6927663463-23.2247767297
21.30987965343-0.5702793418070.06151893064451.204082692590.02121326830081.90786402685-0.0410853598705-0.0401171103020.01001015621660.1128136921980.0232160205053-0.07221352850990.009532786031970.03623199229970.05084373891280.513725303618-0.007228387644640.1001254245460.3416824399870.02028166497370.504137370011-44.68811330923.74869302174-53.6731478326
31.37845947753-0.4983080260910.1497059602781.226445152670.3268479303831.28297493524-0.105780800621-0.1136995733140.1573491132250.1085371957090.072717033395-0.271327437643-0.1389647910210.1400832076210.09176117557070.503425271387-0.003116613872480.08203449651780.3996822706920.003319804459790.554319365951-34.40611139328.25210521315-54.2365806815
41.37991896437-0.05135315986250.2412358696262.330449366531.126872966361.91740733771-0.140051792072-0.1340575780410.2009465479050.3165617040080.387823496763-0.558030210216-0.01861642722540.478817637738-0.006075936817560.5546280050990.0521139311433-0.06990503561380.646247398943-0.09057796050770.708711393298-19.72641537319.0513648905-34.4703962197
51.69025672812-0.892901295203-0.05486798964691.89513232066-0.3150569146151.119872618910.1421625478760.2214538720.177179708532-0.254336553663-0.239200305506-0.0363454360548-0.0950922568647-0.06034920799340.009018781584780.6085585621780.06793580715710.05424249777670.474491191429-0.01703350046410.555579809051-63.114695136926.6199724163-69.9809711304
62.00567815923-0.3198839391320.634502582711.348565115540.1376329750371.471697497-0.169133854935-0.319351505514-0.008825827973940.2913977934850.1363187028860.175877724434-0.0690697995179-0.2824322088080.004648683988250.6502808957280.09568134474830.15911754070.580356884039-0.008862134860720.554971244181-70.872533506224.9873213437-35.8580615063
71.24384337397-1.16600076460.5939640863050.52043207453-0.6147101349460.192546600456-0.453236748079-0.2153156863460.6782010587290.4255540767570.12509353183-0.103963040773-0.264527325077-0.1924066724060.03902923959280.7025519001740.1012482215480.01721226373150.62132279268-0.08724701901510.71655078088-71.224247715835.8293436648-38.2432299708
81.62084877133-0.39879383713-0.5326449349231.30707035661-0.4679119797131.20152794470.000838523255123-0.07665817941330.3937824296-0.0699643385638-0.08909372123680.207809135479-0.305875790232-0.0943655067759-0.04596954718920.574867569940.0779599366999-6.16949599594E-50.553063919343-0.06471964929580.712427343788-80.061521463444.2573537336-59.8843217398
91.729641729330.0361790869164-1.174039878431.56792176965-0.3561996508811.70690592967-0.0444316154370.9096422650320.243746843993-0.1260393595130.236802884680.1468779911830.010901465778-0.9043207052770.05160462397740.503383979531-0.02831487441960.01842504447181.19624791630.1759283469580.547639737931-39.87567957135.63392032262-123.025395901
102.229853335860.272746281121-0.3140271184230.664583138753-0.1284955728252.14419760538-0.08173255911970.220225183438-0.0224350627680.007519734715160.0517913443210.1159150509770.165282725958-0.2128209142230.07237154716620.500515965811-0.03165859198990.09768684360.4229762984610.02020322678330.483724117119-38.8495932852-2.69429104714-89.0088836214
111.68116735450.907674077655-0.3972343966680.926514208995-0.7382547873931.64263260245-0.02806013662061.092727505550.331886214218-0.05358961576810.2981897423630.2570408851120.085270559062-1.32467439070.1316446967910.486957168009-0.02457707397070.07000857797131.517190112860.218759936920.701235721383-62.29626810682.51921688711-109.883563536
121.116190427780.563334838902-0.1729238738851.175738259880.08205621826571.129478693790.113051732242-0.1847470066150.1619013663190.260663071847-0.05502811239380.11969383838-0.009212393521960.0326103403757-0.06161904426550.528356770081-0.03100728245180.05757904966710.4146505579330.01389963200550.47411666987-14.998075482219.2675437976-79.6734710136
131.007072418390.178117963241-0.2313324117091.33456448070.3984893452772.16106462373-0.05039837771930.0629356499511-0.003463143525310.01274657496920.0747302000236-0.09910196764530.0547074950059-0.123573524867-0.03609460900850.4462343218310.008861319378040.05223604789410.4150202249440.04078964032520.429240621431-8.430957433355.41570035248-111.644680567
141.866377917810.746155874616-0.1442029584420.6359147103290.1283572599911.180223533220.05797087009660.2556994588380.233461424434-0.06470887062020.10011899677-0.0243594904456-0.168817971637-0.0623654051923-0.03465099945240.5025170247760.02776588084240.101987314760.4277486901250.06576124456110.52663187233-5.8272705340516.6086223098-112.199201882
151.72147791908-0.331703195954-0.310231957922.180976273460.5285629724531.295283376680.183494122697-0.03855191005720.280385187028-0.141993938676-0.0182397025757-0.120680071377-0.3346737058470.132564712326-0.1530250489590.463720016718-0.04662603383510.07776396141010.413294561789-0.01266288333780.5126012776194.9039310831229.0257216424-94.1484899776
162.155958005710.33944351032-0.6711534017270.946149636475-0.1145037520941.15890005076-0.02898495871010.2591268948020.3385847046750.1440521221480.09076926705230.319394272349-0.0209108713595-0.5681718874030.1223553842440.549099335249-0.0401072370380.06463084882680.6597565619170.06673087483250.478202722353-47.46524872944.42355554753-90.4700804462
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 155 )AA0 - 1551 - 156
22chain 'A' and (resid 156 through 322 )AA156 - 322157 - 320
33chain 'A' and (resid 323 through 373 )AA323 - 373321 - 371
44chain 'A' and (resid 374 through 589 )AA374 - 589372 - 575
55chain 'B' and (resid 0 through 155 )BB0 - 1551 - 156
66chain 'B' and (resid 156 through 322 )BB156 - 322157 - 323
77chain 'B' and (resid 323 through 373 )BB323 - 373324 - 374
88chain 'B' and (resid 374 through 589 )BB374 - 589375 - 576
99chain 'C' and (resid 0 through 155 )CC0 - 1551 - 156
1010chain 'C' and (resid 156 through 323 )CC156 - 323157 - 319
1111chain 'C' and (resid 374 through 588 )CC374 - 588370 - 568
1212chain 'D' and (resid 0 through 155 )DD0 - 1551 - 156
1313chain 'D' and (resid 156 through 322)DD156 - 322157 - 316
1414chain 'D' and (resid 323 through 373 )DD323 - 373317 - 367
1515chain 'D' and (resid 374 through 589 )DD374 - 589368 - 570
1616chain 'C' and (resid 324 through 373 )CC324 - 373320 - 369

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