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- PDB-6fjl: Structure of IbpS from Dickeya dadantii -

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Basic information

Entry
Database: PDB / ID: 6fjl
TitleStructure of IbpS from Dickeya dadantii
ComponentsABC-type Fe3+ transport system, periplasmic component
KeywordsMETAL BINDING PROTEIN / Substrate binding protein Bacterial effector venus fly-trap
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACETATE ION / ABC-type Fe3+ transport system, periplasmic component
Function and homology information
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.70000035298 Å
AuthorsGueguen-Chaignon, V. / Condemine, G. / Terradot, L.
CitationJournal: Nat Commun / Year: 2019
Title: A secreted metal-binding protein protects necrotrophic phytopathogens from reactive oxygen species.
Authors: Liu, L. / Gueguen-Chaignon, V. / Goncalves, I.R. / Rascle, C. / Rigault, M. / Dellagi, A. / Loisel, E. / Poussereau, N. / Rodrigue, A. / Terradot, L. / Condemine, G.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type Fe3+ transport system, periplasmic component
B: ABC-type Fe3+ transport system, periplasmic component
C: ABC-type Fe3+ transport system, periplasmic component
D: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,61910
Polymers155,3344
Non-polymers2856
Water20,3931132
1
A: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9173
Polymers38,8341
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8932
Polymers38,8341
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8932
Polymers38,8341
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ABC-type Fe3+ transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9173
Polymers38,8341
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.447, 112.313, 78.722
Angle α, β, γ (deg.)90.0, 95.53, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A28 - 139
121chain 'A'A141 - 371
231chain 'B'B28 - 139
241chain 'B'B141 - 371
351chain 'C'C28 - 139
361chain 'C'C141 - 371
471chain 'D'D28 - 139
481chain 'D'D141 - 371

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Components

#1: Protein
ABC-type Fe3+ transport system, periplasmic component


Mass: 38833.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: Dda3937_02937 / Plasmid: pGEX-6p3 / Production host: Escherichia coli (E. coli) / Variant (production host): NM522 / References: UniProt: E0SCP7
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 24% PEG 4000 Cacodylate Na 50 mM pH 6 Magnesium Acetate 80 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97301 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97301 Å / Relative weight: 1
ReflectionResolution: 1.7→47.55 Å / Num. obs: 146429 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.9350094583 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.793.30.6111.2212850.3920.7280.61199.4
1.79-1.93.40.4061.7201770.2550.4810.40699.7
1.9-2.033.50.252.9190140.1560.2960.2599.9
2.03-2.193.30.1624.1176010.1040.1930.16299.3
2.19-2.43.60.1155.8163070.0710.1350.11599.9
2.4-2.693.50.0827.8147440.0510.0970.08299.8
2.69-3.13.40.05910.7129970.0370.0690.05999.7
3.1-3.83.50.04314.2110020.0270.0510.04399.9
3.8-5.383.40.03119.685620.0190.0370.03199.7
5.38-47.5473.40.02322.247400.0140.0270.02399.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.70000035298→47.5465786313 Å / SU ML: 0.216352520644 / Cross valid method: THROUGHOUT / σ(F): 1.33259982426 / Phase error: 26.6192617955
RfactorNum. reflection% reflectionSelection details
Rfree0.205859044668 7358 5.0372419081 %RANDOM
Rwork0.174517748023 138714 --
obs0.17613569009 146072 99.4221384281 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.1333890265 Å2
Refinement stepCycle: LAST / Resolution: 1.70000035298→47.5465786313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10947 0 18 1132 12097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065250982945411327
X-RAY DIFFRACTIONf_angle_d1.0279971061815478
X-RAY DIFFRACTIONf_chiral_restr0.04483663513251650
X-RAY DIFFRACTIONf_plane_restr0.005570883636892024
X-RAY DIFFRACTIONf_dihedral_angle_d12.74872805724058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.3805119873382350.3409438226024599X-RAY DIFFRACTION98.9965185337
1.7193-1.73950.3267350589812180.3078857574044579X-RAY DIFFRACTION98.7240172875
1.7395-1.76080.3346109629552410.3031385240774602X-RAY DIFFRACTION98.6756316218
1.7608-1.78310.3321404728432100.2935260774054580X-RAY DIFFRACTION98.3774902444
1.7831-1.80650.3338384407362600.2879492461334535X-RAY DIFFRACTION97.9971387697
1.8065-1.83130.2908777676532230.2610310350484641X-RAY DIFFRACTION99.5090016367
1.8313-1.85740.3103467249382530.2449786182224591X-RAY DIFFRACTION99.732345069
1.8574-1.88520.3004973443612370.2442692955524611X-RAY DIFFRACTION99.5686999384
1.8852-1.91460.2717199694722690.2352766208234619X-RAY DIFFRACTION99.5722143003
1.9146-1.9460.2631723760862560.2214031619434599X-RAY DIFFRACTION99.569319114
1.946-1.97960.2701068214272680.2200810167914598X-RAY DIFFRACTION99.6314496314
1.9796-2.01560.2602884283322880.2255128153834613X-RAY DIFFRACTION99.7963754836
2.0156-2.05430.245695455112240.2201512148644598X-RAY DIFFRACTION99.3816982688
2.0543-2.09630.2316092993212050.204920900694663X-RAY DIFFRACTION99.1647993481
2.0963-2.14180.2462611803382440.2005074943994620X-RAY DIFFRACTION99.042964773
2.1418-2.19170.2440719953772250.1953434693544569X-RAY DIFFRACTION99.0905332782
2.1917-2.24650.222158891552470.1880873742964647X-RAY DIFFRACTION99.7554015491
2.2465-2.30720.2356993510612700.1915981162134622X-RAY DIFFRACTION99.67400163
2.3072-2.37510.2667046889882290.1946480372014633X-RAY DIFFRACTION99.8152330117
2.3751-2.45170.2248804179552540.1866810978084650X-RAY DIFFRACTION99.7964997965
2.4517-2.53940.221582514042150.1806920510284653X-RAY DIFFRACTION99.7132322819
2.5394-2.6410.199589365962500.181527703494630X-RAY DIFFRACTION99.5512035904
2.641-2.76120.1985085491392560.1719610788594619X-RAY DIFFRACTION99.3073945814
2.7612-2.90680.2061400967762370.1842844040554651X-RAY DIFFRACTION99.5925020375
2.9068-3.08890.2255319403052430.1782769661594658X-RAY DIFFRACTION99.9592086478
3.0889-3.32730.2104225264912690.1741409558334619X-RAY DIFFRACTION99.8162140086
3.3273-3.6620.1769532234922850.1563798114834631X-RAY DIFFRACTION99.77674041
3.662-4.19170.1473704526482650.1288844492424630X-RAY DIFFRACTION99.5728234337
4.1917-5.280.1446948924072120.1218393437114739X-RAY DIFFRACTION99.9596204321
5.28-47.56520.1574377051572700.1303701579064715X-RAY DIFFRACTION99.5606151388
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.39724444524-0.3425201681930.1390522503811.377668197021.373936135462.0698746219-0.05397727282040.2269380259130.17534075572-0.534096490259-0.0206891279251-0.0846536637112-0.7528557072210.1982879723030.09162534556050.418881432883-0.121349917246-0.02294801471480.2463134142540.07308850089770.2852831972360.88835693275914.5575871409-12.0888074859
20.872560923297-0.1819259969660.2165304226461.325519104830.6716015380822.87539379746-0.05225620159750.0764039567355-0.1242884346880.101212827012-0.1686114306240.2089427635440.519288300838-0.3535988145310.1644700368810.249057549079-0.1073468587110.04670566367410.244564541275-0.04465534753290.264474672065-10.1730859548-10.8409611584-12.9734646834
30.551468499592-0.1170481751080.1454966967161.138348016761.028653294383.01733372449-0.07531933080860.06973259294140.0442155609613-0.161075965019-0.1253800382060.00648537107229-0.323722363314-0.09410164816380.1563897425360.200101632764-0.0640285341243-0.02671993539630.1900578828020.01724384631870.238693971806-6.209119364815.03482343031-11.5889226268
41.64784300044-0.1524259693240.1547055064951.053882733340.007874419016821.118165677480.105200738755-0.225485147090.1360325216160.144898487781-0.0847688900335-0.127318774613-0.4202648008370.304821670102-0.01708237025880.363564356461-0.1689963937720.007995980240890.295793498719-0.007812781008790.244340111713-13.588134507832.1963479088-49.8346891631
52.088910528790.156209201492-0.3872376297711.0880213068-0.423795545041.051583663820.139505842146-0.08758459035460.05573567458440.306512667568-0.05203903143180.0977817385315-0.295774611032-0.059102204755-0.07269554580490.25360114306-0.03715240647420.02659261252830.1795767106130.01020241810630.181781233433-38.939356172121.4590298269-53.0543741212
61.324501557080.236772264191-0.003786678335180.4753558273010.03627116346551.318201072220.124236083193-0.1146869136130.06587526073370.152770237968-0.0931716313253-0.0664036862998-0.3358579119120.145135766101-0.0339196427840.260959781828-0.0951037124054-0.002694458557210.2146225007660.01668235571840.22763825138-22.661557521525.5737597808-52.3058904911
71.090957837350.09826378816220.05094435403950.3547228175160.1430308550351.41982563802-0.1888763395861.01643214271-0.11154834203-0.4731883506820.2589448359010.1723063856720.148937418761-0.50913909076-0.05276032124660.314579188075-0.237286769292-0.06437525061380.953653733709-0.03062534027850.326097774161-46.3161452515.4079371799-21.0094090562
80.8166281153020.314762864065-0.2491592211381.318298795590.04179376232870.550642645269-0.1164563811530.469821959514-0.0652352641589-0.064666218580.1061148143510.01846609456280.14433391531-0.364376961201-0.01417164260680.149083092985-0.0876346935777-0.02141455946060.487838453763-0.02264945813620.255280811975-39.728061935514.8347937273-9.6400606307
91.168799329980.433820161672-0.474810228781.42581619318-0.1681404578762.437483420620.01129206612950.3378258126560.188924449998-0.04741073845920.1400517199460.136784133317-0.624778208598-0.127884759965-0.1331798675060.30884391416-0.0176293638424-0.0001601912509920.3549766157720.08704597863330.236352090854-30.581703852837.0305505669-10.4378504435
101.037909717650.411650399951-0.4253348944510.829677114727-0.2395220931121.96662508672-0.06334477741990.404219465384-0.0335350853186-0.08354489075820.13957634690.0527440443113-0.109990752847-0.28506239842-0.07038490631940.1928441852-0.055551834859-0.01130575189360.4134180389770.02538906212920.248202282473-34.058401663525.2214594101-11.7783577069
110.959962343046-0.6479354571630.5928017203462.67276563128-0.3558861371610.5536721909020.0124298292942-0.0444674657865-0.280405457-0.05578792606930.06160615668850.4505442254420.638488898486-0.600429931058-0.07697229144270.990252010422-0.3727043957230.1936770584770.565564601679-0.04671782966020.5045324308-23.7854745486-13.4209835425-41.928086083
121.189363594636.46697404035E-5-0.1694676034221.093203686330.3447967900381.07534146656-0.1685137307490.49219840817-0.3579673722180.81956031338-0.0786458740090.007089913358811.23759931411-0.06380023054620.3558596242371.06986388318-0.3221345844910.160546560053-0.0600340619663-0.03924522622930.357587119942-7.47804300614-14.937789935-54.2108927072
131.616170473910.3351015793660.02462749541042.053041200310.555556049740.168847970259-0.2691589065810.304348637966-0.09726458769490.181201564206-0.181233934310.1835323530660.664380883162-0.8214444662030.2285797164370.503172385485-0.2951518029350.09619145225040.40745907815-0.08652129279210.313343763353-13.7302729965-6.27052249723-60.468153217
141.222380678110.5216356175310.4790469839071.870099041680.4912215981760.238949449441-0.1898008914240.11350442025-0.04099595051580.402407678742-0.2004558155630.2656988284320.642146000551-0.7423556754080.2701225093690.444429992912-0.2438736411830.1112154150030.437427247606-0.06931688629340.379309403022-18.055993261-0.188434891521-47.3359489681
153.216817050620.0340624995925-0.1870470972741.235203827370.4046535062792.283618045260.0774969547848-0.237562413398-0.005417617843010.221310660963-0.1051110580520.02653234913730.50598636234-0.1129242522620.1264452629060.358092747534-0.03881096002750.009539414275920.171806503571-0.01197009281490.2284961368950.894667074198-0.159015276819-47.6062376567
161.86310824895-0.04034274230850.02397070127771.750927135180.5112368248542.73300378179-0.0441517326348-0.0490617564577-0.0008813116199970.1497423650030.0425092698365-0.1565029002050.3134617136560.3635117925630.01223027042260.1961802368220.0128682433386-0.02877375331790.2046363146620.02012004501580.2070527827314.77876889364.10995006541-56.4826345764
171.688862399320.287732224804-0.3006788519631.096778162040.1352766953151.85420488578-0.112100182641-0.0253257672501-0.1988022841530.338613824239-0.006277285515220.07847173828660.878821472077-0.05550703634110.04122800717360.527040371465-0.09107411578050.05976074855920.123200183342-0.004969517784170.2422829132-1.0812202959-4.27136409206-48.1993084188
181.222751959480.068411811959-0.4853758624870.2249525060780.6199701808221.93235827532-0.0540016662389-0.0627470240641-0.1284367372960.1611292436350.03741828362080.03286347267480.603352976593-0.1529860163120.06487345240720.321314938553-0.06116543584950.01908109967250.181648588633-0.01082686326040.270492692484-4.232727566613.5895232847-44.1743764113
191.620896976070.380489615662-0.3670140772080.847868044987-0.1110386251070.973482924651-0.1616149286920.198768338604-0.2218352377820.1266960474310.004649630849670.02744686076260.751102933127-0.1392572590150.1006524918990.439731075914-0.08006523869370.03779345503310.186595427647-0.0403056560970.2458927911443.19695791845-5.88803475324-66.6090139327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 372 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 139 )
5X-RAY DIFFRACTION5chain 'B' and (resid 140 through 265 )
6X-RAY DIFFRACTION6chain 'B' and (resid 266 through 372 )
7X-RAY DIFFRACTION7chain 'C' and (resid 28 through 73 )
8X-RAY DIFFRACTION8chain 'C' and (resid 74 through 139 )
9X-RAY DIFFRACTION9chain 'C' and (resid 140 through 280 )
10X-RAY DIFFRACTION10chain 'C' and (resid 281 through 372 )
11X-RAY DIFFRACTION11chain 'D' and (resid 28 through 47 )
12X-RAY DIFFRACTION12chain 'D' and (resid 48 through 99 )
13X-RAY DIFFRACTION13chain 'D' and (resid 100 through 121 )
14X-RAY DIFFRACTION14chain 'D' and (resid 122 through 139 )
15X-RAY DIFFRACTION15chain 'D' and (resid 140 through 164 )
16X-RAY DIFFRACTION16chain 'D' and (resid 165 through 233 )
17X-RAY DIFFRACTION17chain 'D' and (resid 234 through 291 )
18X-RAY DIFFRACTION18chain 'D' and (resid 292 through 336 )
19X-RAY DIFFRACTION19chain 'D' and (resid 337 through 372 )

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