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- PDB-6eby: Crystal structure of the MbtH-like protein FscK bound to the inte... -

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Basic information

Entry
Database: PDB / ID: 6eby
TitleCrystal structure of the MbtH-like protein FscK bound to the interface forming region of FscH adenylation domain from Thermobifida fusca
Components
  • Amino acid adenylation
  • Conserved protein MbtH
KeywordsPROTEIN BINDING / MbtH-like protein / adenylation domain / domain activation
Function / homology
Function and homology information


amide biosynthetic process / small molecule metabolic process / : / lipid biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Luciferase; domain 3 / Luciferase; Domain 3 / Condensation domain ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Luciferase; domain 3 / Luciferase; Domain 3 / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amino acid adenylation / Putative conserved protein MbtH
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBruner, S.D. / Zagulyaeva, A.A.
CitationJournal: To Be Published
Title: Comprehensive analysis of protein-protein interactions between MbtH-like protein FscK and adenylation domains in nonribosomal biosynthesis of Fuscachelins.
Authors: Bruner, S.D. / Zagulyaeva, A.A.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein MbtH
B: Amino acid adenylation
C: Conserved protein MbtH
D: Amino acid adenylation


Theoretical massNumber of molelcules
Total (without water)34,7734
Polymers34,7734
Non-polymers00
Water3,513195
1
A: Conserved protein MbtH
B: Amino acid adenylation


Theoretical massNumber of molelcules
Total (without water)17,3862
Polymers17,3862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area7390 Å2
MethodPISA
2
C: Conserved protein MbtH
D: Amino acid adenylation


Theoretical massNumber of molelcules
Total (without water)17,3862
Polymers17,3862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-10 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 58.290, 58.700
Angle α, β, γ (deg.)90.000, 107.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Conserved protein MbtH


Mass: 9094.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1863 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS3
#2: Protein Amino acid adenylation


Mass: 8291.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1866 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, sodium chloride, BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→58.29 Å / Num. obs: 23530 / % possible obs: 98.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 16.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Rrim(I) all: 0.077 / Net I/σ(I): 17.9 / Num. measured all: 180172 / Scaling rejects: 249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.897.70.22614630.980.0870.24296.9
9.06-58.296.40.0532230.9950.0220.05798.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EA3
Resolution: 1.85→29.452 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.73
RfactorNum. reflection% reflection
Rfree0.2346 3909 8.49 %
Rwork0.2003 --
obs0.2031 46031 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.4 Å2 / Biso mean: 21.0742 Å2 / Biso min: 4.29 Å2
Refinement stepCycle: final / Resolution: 1.85→29.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 195 2249
Biso mean---26.5 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022110
X-RAY DIFFRACTIONf_angle_d0.582880
X-RAY DIFFRACTIONf_chiral_restr0.043304
X-RAY DIFFRACTIONf_plane_restr0.004384
X-RAY DIFFRACTIONf_dihedral_angle_d17.745756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87260.24541510.22691530168196
1.8726-1.89630.26211520.21411431158397
1.8963-1.92120.22471580.21241472163097
1.9212-1.94750.2811230.21611501162497
1.9475-1.97540.25921120.20651603171597
1.9754-2.00480.24261490.19921395154497
2.0048-2.03620.21361190.20161504162398
2.0362-2.06950.23391660.20331562172897
2.0695-2.10520.23971430.19661425156898
2.1052-2.14350.27071310.19541480161197
2.1435-2.18470.22471310.19631570170198
2.1847-2.22930.29311400.20121456159697
2.2293-2.27770.20911350.19381535167098
2.2777-2.33070.22111360.20071472160898
2.3307-2.38890.27071200.20131489160998
2.3889-2.45350.27871710.22181512168398
2.4535-2.52570.22371250.20611514163998
2.5257-2.60710.23191560.20881477163398
2.6071-2.70030.27581430.21481538168198
2.7003-2.80830.23911360.20011537167398
2.8083-2.9360.23581380.21451486162499
2.936-3.09060.23211350.20761540167599
3.0906-3.2840.19921320.20851501163399
3.284-3.53720.2371470.19611495164299
3.5372-3.89250.23241390.18941544168399
3.8925-4.4540.17921320.16771517164999
4.454-5.60530.2011470.18361520166799
5.6053-29.45590.28131420.21991516165899
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)
10.0161-0.03220.02620.0937-0.12160.1316-0.03670.18150.1339-0.13490.10420.2535-0.1344-0.13160.03820.1023-0.0448-0.01220.1487-0.01350.1363-68.211944.049778.452
20.1025-0.00470.07020.11160.16190.23970.1096-0.2204-0.16710.05290.0137-0.08330.2754-0.30120.03740.1241-0.0399-0.02750.13810.0340.1156-67.96842.600687.8148
30.09930.0401-0.20330.0531-0.17810.63230.0225-0.15050.11450.45870.3003-0.412-0.2519-0.01960.04360.13780.0002-0.06010.1127-0.05810.198-55.151551.562795.3633
40.0009-0.00630.03570.0136-0.05120.2841-0.0223-0.3869-0.302-0.08610.0883-0.0784-0.0936-0.32120.02480.067-0.0094-0.0050.11650.00090.082-62.980245.510688.0814
50.2130.29380.15410.72160.65760.88640.1525-0.2122-0.58880.04160.2634-0.16380.21020.1660.10430.1678-0.00490.00550.06290.07760.1679-62.249335.879286.989
60.0670.158-0.00910.5187-0.0460.01270.1045-0.426-0.0010.0747-0.0561-0.4948-0.1619-0.11030.0155-0.13130.1907-0.27010.01370.12770.0088-55.653642.910793.3243
70.1256-0.04880.00550.02590.03780.03060.2969-0.1112-0.43010.233-0.16460.14260.2283-0.2736-0.00550.1508-0.0428-0.02520.13880.07830.1076-69.648942.798993.3349
80.01640.01050.00050.0223-0.00310.02180.0122-0.09520.14910.11860.06120.1314-0.2965-0.0807-00.12940.00050.01080.21830.03470.1711-72.540749.308687.3077
90.72350.04490.42450.01270.0340.2634-0.0201-0.32970.21650.1113-0.06890.1738-0.1432-0.377-0.08230.162-0.0010.03480.1206-0.01220.0575-67.188154.354193.9415
100.04520.06710.14320.31080.24070.6064-0.0973-0.4240.22740.12280.2077-0.16110.15590.20450.05390.0540.04130.01080.2001-0.06510.171-46.753147.147676.8453
110.0143-0.0254-0.00740.02890.01570.02440.0553-0.0313-0.1708-0.0105-0.0326-0.03050.6392-0.00250.00520.159-0.0044-0.0010.08360.00120.0763-58.195738.107975.6647
120.06810.01460.07080.00850.03930.1720.07520.06880.0649-0.0287-0.1382-0.10640.0759-0.2056-0.00240.14920.01090.01550.0641-0.00250.1252-54.007635.690470.1372
130.1036-0.0516-0.04990.0551-0.02950.0366-0.0679-0.2121-0.22050.03550.0304-0.0914-0.23770.0370.00160.0807-0.0157-0.00630.0659-0.01090.0872-53.876147.690976.5408
140.07130.0232-0.02650.14550.05880.2968-0.3307-0.50170.09530.343-0.0585-0.24880.12460.2141-0.35710.2199-0.0317-0.16180.1384-0.01570.2637-53.660560.243189.1975
150.03750.0053-0.01820.01320.02230.03170.0376-0.06720.125-0.20420.11830.13130.0015-0.13540.00470.1390.0214-0.00550.17410.02520.1177-65.218358.700485.8653
160.02850.01040.05440.1795-0.15750.34840.0329-0.0897-0.07820.19050.0246-0.0086-0.0850.03750.02490.0634-0.0049-0.01140.0722-0.00190.1277-57.636447.840283.0783
170.10240.053-0.10040.07430.00190.18340.32420.0519-0.00340.03730.04630.086-0.00450.33260.07940.05960.0256-0.01260.1422-0.00150.1008-52.341947.986785.0728
180.05430.012-0.00910.01810.03630.02430.0368-0.09370.0568-0.08940.140.01790.2295-0.09810.01110.1214-0.0005-0.01360.08380.00520.0935-58.813447.559171.0643
19-0.0034-0.0048-0.00940.202-0.27370.3259-0.14510.0905-0.0225-0.0612-0.1526-0.03780.28330.3596-0.07840.18070.0921-0.01560.1668-0.01130.1259-47.310140.006764.5108
200.07740.047-0.02360.0738-0.07460.07030.0422-0.0078-0.20210.1089-0.03850.0763-0.17390.12940.01830.16020.0018-0.00240.1214-0.03260.1184-55.951247.176864.7522
210.03350.06170.10420.42180.23590.34230.2321-0.2124-0.00350.0157-0.09070.3001-0.0684-0.3293-0.01490.16280.01260.01550.13610.05480.119-61.884763.722462.4295
220.0844-0.033-0.01260.34480.09930.0170.0150.0516-0.00850.03060.0482-0.04640.005-0.23530.03850.152-0.02070.00530.16060.05810.0912-59.96865.246354.4688
230.0152-0.0098-0.0048-0.00040.00770.0229-0.05760.2212-0.3444-0.1177-0.3292-0.20560.3531-0.0082-0.0050.14850.04550.05270.28110.01260.222-42.719156.789554.1995
240.19410.15720.0950.11390.08770.045-0.08860.37710.08730.08350.1085-0.0504-0.14760.34970.00620.1240.02280.01510.18660.01940.0887-52.51362.411356.2377
250.5434-0.1293-0.06610.06890.15850.3819-0.09280.10110.20040.1143-0.0568-0.2676-0.44960.3721-0.03540.2013-0.05880.01760.13860.07430.2299-49.006570.301959.2461
260.01310.10790.04550.97370.35880.11340.1832-0.14330.17680.04580.5107-0.457-0.22150.36430.28720.0277-0.01190.26610.33730.14070.0159-46.177663.386552.6621
270.18810.03130.4560.00110.07411.0698-0.11-0.01370.2347-0.1722-0.4218-0.1489-0.0171-0.1727-0.24170.2098-0.01610.01140.18930.12220.0999-59.254163.944950.0163
280.0254-0.007-0.00230.00470.00650.0341-0.06480.0955-0.2315-0.26060.21430.04430.15840.00060.00240.2095-0.0418-0.01320.24440.03810.1047-58.888857.507949.3335
290.03890.06360.01680.1310.08140.0324-0.15640.3006-0.1394-0.27120.00420.09890.33490.4318-0.08210.35220.05790.1370.2174-0.009-0.565-53.029152.206949.7922
300.0120.0015-0.01140.01630.00630.0117-0.0518-0.0402-0.20830.12280.1323-0.25290.10530.409200.14790.0203-0.02630.2326-0.0130.1831-47.194861.225675.1203
310.6115-0.2664-0.70680.12550.3070.84430.2218-0.17520.5183-0.45140.27620.1982-0.62320.15360.08020.19650.01170.02470.05040.03640.1506-56.052970.894968.5049
320.049-0.03190.14250.1835-0.10650.5691-0.0161-0.01350.0718-0.11730.12910.13-0.04240.36090.05990.0541-0.03430.01380.04860.00860.1058-55.962768.041475.7327
330.1944-0.076-0.25690.4271-0.1910.45240.16290.0609-0.08620.1570.1218-0.13410.00980.16490.1370.05590.0343-0.00090.1318-0.07860.1563-46.447954.111568.263
340.31780.2144-0.01490.1651-0.04960.0294-0.0722-0.015-0.4135-0.17490.1398-0.31660.43770.3763-0.00190.27170.0054-0.00560.2573-0.05350.1774-49.863946.372957.6569
350.1632-0.1548-0.1760.19140.19970.19640.16810.1440.2685-0.35340.29680.2041-0.0433-0.12970.01720.150.0127-0.00730.17850.03440.1479-56.838254.230560.7046
360.0117-0.04350.00250.1464-0.13080.180.05150.17630.0620.0101-0.00870.12980.08410.15750.00420.0707-0.02920.01330.08070.0160.1204-48.699262.468464.9599
370.17870.0089-0.150.113-0.09350.14150.2703-0.19170.14890.019-0.11040.0416-0.05030.21640.02730.0741-0.0331-0.01440.15020.00250.0958-49.353759.219666.1607
380.00340.0021-0.02630.0383-0.07330.28630.08320.027-0.0543-0.02920.2092-0.26940.00620.31010.0150.0553-0.00830.0130.0637-0.02420.098-58.13364.190279.2501
390.05250.035-0.03660.0435-0.07990.22080.197-0.12630.04470.1998-0.23740.0686-0.35480.273-0.00960.1197-0.0303-0.01860.0913-0.03740.1671-53.401365.621585.7933
400.0139-0.01240.01480.00030.0103-0.0088-0.0546-0.013-0.0008-0.1641-0.06030.1295-0.062-0.0631-0.00480.111-0.0081-0.03450.0775-0.0310.124-63.251958.918577.4115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:8)A3 - 8
2X-RAY DIFFRACTION2(chain A and resid 9:16)A9 - 16
3X-RAY DIFFRACTION3(chain A and resid 17:21)A17 - 21
4X-RAY DIFFRACTION4(chain A and resid 22:26)A22 - 26
5X-RAY DIFFRACTION5(chain A and resid 27:31)A27 - 31
6X-RAY DIFFRACTION6(chain A and resid 32:36)A32 - 36
7X-RAY DIFFRACTION7(chain A and resid 37:43)A37 - 43
8X-RAY DIFFRACTION8(chain A and resid 44:49)A44 - 49
9X-RAY DIFFRACTION9(chain A and resid 50:56)A50 - 56
10X-RAY DIFFRACTION10(chain B and resid 378:382)B378 - 382
11X-RAY DIFFRACTION11(chain B and resid 383:388)B383 - 388
12X-RAY DIFFRACTION12(chain B and resid 389:397)B389 - 397
13X-RAY DIFFRACTION13(chain B and resid 398:404)B398 - 404
14X-RAY DIFFRACTION14(chain B and resid 405:410)B405 - 410
15X-RAY DIFFRACTION15(chain B and resid 411:416)B411 - 416
16X-RAY DIFFRACTION16(chain B and resid 417:426)B417 - 426
17X-RAY DIFFRACTION17(chain B and resid 427:434)B427 - 434
18X-RAY DIFFRACTION18(chain B and resid 435:440)B435 - 440
19X-RAY DIFFRACTION19(chain B and resid 441:446)B441 - 446
20X-RAY DIFFRACTION20(chain B and resid 447:454)B447 - 454
21X-RAY DIFFRACTION21(chain C and resid 3:7)C3 - 7
22X-RAY DIFFRACTION22(chain C and resid 8:15)C8 - 15
23X-RAY DIFFRACTION23(chain C and resid 16:20)C16 - 20
24X-RAY DIFFRACTION24(chain C and resid 21:27)C21 - 27
25X-RAY DIFFRACTION25(chain C and resid 28:33)C28 - 33
26X-RAY DIFFRACTION26(chain C and resid 34:38)C34 - 38
27X-RAY DIFFRACTION27(chain C and resid 39:44)C39 - 44
28X-RAY DIFFRACTION28(chain C and resid 45:50)C45 - 50
29X-RAY DIFFRACTION29(chain C and resid 51:56)C51 - 56
30X-RAY DIFFRACTION30(chain D and resid 378:383)D378 - 383
31X-RAY DIFFRACTION31(chain D and resid 384:389)D384 - 389
32X-RAY DIFFRACTION32(chain D and resid 390:400)D390 - 400
33X-RAY DIFFRACTION33(chain D and resid 401:406)D401 - 406
34X-RAY DIFFRACTION34(chain D and resid 407:414)D407 - 414
35X-RAY DIFFRACTION35(chain D and resid 415:420)D415 - 420
36X-RAY DIFFRACTION36(chain D and resid 421:426)D421 - 426
37X-RAY DIFFRACTION37(chain D and resid 427:437)D427 - 437
38X-RAY DIFFRACTION38(chain D and resid 438:442)D438 - 442
39X-RAY DIFFRACTION39(chain D and resid 443:449)D443 - 449
40X-RAY DIFFRACTION40(chain D and resid 450:454)D450 - 454

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