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- PDB-6mlk: Structure of Thioesterase from DEBS with a thioesterase-specific ... -

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Basic information

Entry
Database: PDB / ID: 6mlk
TitleStructure of Thioesterase from DEBS with a thioesterase-specific antibody
Components
  • 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
  • Heavy chain of Fab 3A6
  • Light chain of Fab 3A6
KeywordsTRANSFERASE / 6-Deoxyerythronolide B synthase / Thioesterase / monoclonal antibody
Function / homology
Function and homology information


erythronolide synthase activity / 6-deoxyerythronolide-B synthase / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 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, catalytic domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Erythronolide synthase EryA3
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMathews, I.I. / Li, X. / Khosla, C.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM087934 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41CA196276 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM104659 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Department of Energy (DOE, United States)P41GM103393 United States
CitationJournal: Biochemistry / Year: 2018
Title: Discovery and Characterization of a Thioesterase-Specific Monoclonal Antibody That Recognizes the 6-Deoxyerythronolide B Synthase.
Authors: Li, X. / Sevillano, N. / La Greca, F. / Hsu, J. / Mathews, I.I. / Matsui, T. / Craik, C.S. / Khosla, C.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
L: Light chain of Fab 3A6
H: Heavy chain of Fab 3A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4414
Polymers84,4053
Non-polymers351
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-39 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.580, 172.580, 159.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11H-419-

HOH

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Components

#1: Protein 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 / DEBS 3 / 6-deoxyerythronolide B synthase III / Erythronolide synthase / ORF C


Mass: 32112.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q03133, 6-deoxyerythronolide-B synthase
#2: Antibody Light chain of Fab 3A6


Mass: 25772.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Antibody Heavy chain of Fab 3A6


Mass: 26519.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 15% Ethylene glycol, 0.2M Na2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.45→38.426 Å / Num. obs: 33435 / % possible obs: 99.8 % / Redundancy: 9.519 % / Biso Wilson estimate: 63.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.095 / Χ2: 1.112 / Net I/σ(I): 14.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.516.3340.858224590.7380.934100
2.51-2.5810.3370.8632.7123860.8570.907100
2.58-2.6610.2230.6323.6123180.9150.665100
2.66-2.749.9680.4984.5522610.9390.525100
2.74-2.839.1490.3845.5322150.9470.40899.8
2.83-2.9310.5270.2947.6121100.9780.309100
2.93-3.0410.5560.2259.8820630.9850.236100
3.04-3.1610.3920.17112.719770.9890.17999.9
3.16-3.310.2580.14515.6318880.9910.152100
3.3-3.469.8830.11818.2418160.9930.125100
3.46-3.658.9770.09920.0217170.9940.10599.5
3.65-3.879.4140.09123.2616290.9940.09699.8
3.87-4.149.6440.08125.1615430.9970.08699.9
4.14-4.479.2670.07526.8514410.9960.0899.9
4.47-4.99.0330.06927.6313460.9970.07399.9
4.9-5.488.2860.06726.6411710.9970.07198.6
5.48-6.339.6270.06328.5210800.9980.06699.9
6.33-7.759.4220.05929.629010.9980.06299.9
7.75-10.968.6290.04829.527080.9980.05197.7
10.96-38.4269.480.04531.674060.9990.04796.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB codes: 1MN6 and 4LRI

1mn6

4lri


Resolution: 2.45→38.426 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.28
RfactorNum. reflection% reflection
Rfree0.2352 1671 5 %
Rwork0.1749 --
obs0.1779 33432 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.57 Å2 / Biso mean: 70.5827 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.45→38.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 1 65 5291
Biso mean--85.56 64 -
Num. residues----687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.52210.38551380.314226152753100
2.5221-2.60350.34561380.259326412779100
2.6035-2.69650.30621390.239426282767100
2.6965-2.80440.31481370.235226092746100
2.8044-2.9320.27871390.234326282767100
2.932-3.08650.31381390.212826412780100
3.0865-3.27980.26531380.204526322770100
3.2798-3.53290.27341400.192826622802100
3.5329-3.88810.23361390.169826482787100
3.8881-4.450.22381400.144126422782100
4.45-5.60380.16141400.1352676281699
5.6038-38.43060.21211440.15832739288399
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)
10.7135-0.28640.15410.1186-0.11220.3632-0.0198-0.056-0.00190.01620.01180.12690.4343-0.429-0.11340.9327-0.23230.02470.48620.00990.529115.074817.7999-68.0278
20.17540.05810.13480.02960.0760.159-0.2616-0.3149-0.2376-0.04160.23490.34980.4195-0.6617-0.01271.02-0.19380.12080.60240.09050.510314.408813.2386-54.1232
30.1359-0.0841-0.10240.0397-0.16620.4532-0.3213-0.1422-0.0390.03660.153-0.09910.27620.0406-0.00050.9326-0.05720.01580.4339-0.01510.508923.576618.6275-59.0574
40.02360.0672-0.02710.0651-0.04860.05130.0312-0.31710.03210.2791-0.14440.01060.27110.4953-0.00030.83490.07410.03370.52770.03470.490338.184117.9498-59.5802
50.07490.0265-0.0310.0178-0.03690.02750.3105-0.1457-0.3104-0.1723-0.04440.09320.17980.167901.41570.09120.02880.58920.05820.712631.3546.606-52.5894
60.8938-0.2938-0.3020.37490.19790.4825-0.94980.206-0.2984-0.09150.2853-0.1651.0024-0.2772-0.081.3236-0.16280.26930.0470.08490.614345.389911.0863-88.8997
70.8381-0.0869-0.06960.25750.09660.0104-0.98960.1911-0.36840.27970.1280.01661.0115-0.2568-0.59481.4953-0.30410.3551-0.011-0.03710.572544.80879.624-93.5555
81.5912-0.1833-0.66670.5195-0.26890.5798-0.28510.4910.02950.26890.31650.00710.3116-0.18760.07290.6762-0.04470.01830.1936-0.02090.418356.736924.559-104.1165
90.02850.0344-0.02260.04170.06460.1061-0.00060.40370.2064-0.2208-0.00920.06660.54060.04780.00070.5407-0.0332-0.02510.44680.00740.541864.069325.0915-115.8441
100.0724-0.11640.01110.24170.06310.10550.45510.5339-0.08820.2065-0.3232-0.26440.61610.02310.00080.6529-0.0027-0.04020.56380.02210.673962.016624.6001-112.1746
110.0517-0.0025-0.04770.0026-0.01380.15790.04890.20570.0982-0.22850.0593-0.19230.08050.202800.551-0.04520.14870.63380.04350.691669.569730.5911-121.1316
120.77530.1999-0.15170.04570.10950.32260.1984-0.48050.34020.4080.21050.1713-0.22240.31670.00320.6260.0452-0.09660.42870.09420.689851.832338.4752-85.2919
130.0184-0.0468-0.01070.08160.05170.1017-0.11640.10970.4698-0.04230.14560.29520.219-0.1053-0.00010.6481-0.0091-0.07650.47970.06230.689939.880132.6993-80.0384
140.03480.04730.02510.00530.04610.0767-0.1614-0.1384-0.1832-0.3868-0.02650.0530.21260.02860.00020.72940.00360.12480.37990.01390.528152.532526.0936-85.3452
150.02850.02140.01470.0459-0.03680.04520.0846-0.568-0.04450.2705-0.24890.18230.2175-0.10250.00020.65730.08190.03140.425-0.00920.458146.456127.2477-73.3593
160.02820.0369-0.0560.03810.00430.17010.2018-0.33430.32440.2021-0.1480.4249-0.03680.200200.59840.0628-0.08660.4387-0.02290.646550.058932.4659-73.5847
170.00590.0129-0.0030.0237-0.03540.0669-0.0724-0.1060.1144-0.161-0.02660.24530.19470.3473-0.00610.54610.0750.01940.5631-0.10410.601254.404534.7792-79.6314
180.04560.04750.0079-0.03570.00140.0714-0.14120.1233-0.29780.29030.0674-0.02580.38480.1039-0.00010.7502-0.00690.12310.31020.05750.509641.614623.5282-83.9525
190.1258-0.0933-0.06810.03220.04390.17380.06360.13590.1641-0.05210.06220.01550.384-0.06630.00030.536-0.0322-0.09060.45810.03230.583255.122336.3673-91.5022
200.0826-0.1078-0.03340.07470.03970.01470.16030.51110.092-0.0498-0.2094-0.0813-0.01140.1072-0.00020.37450.0178-0.04340.45590.07350.51558.475739.4523-114.6218
210.1409-0.0994-0.19850.40420.18570.20450.07420.1620.05870.0248-0.26760.0920.0678-0.2474-0.00020.4072-0.0509-0.04480.51580.09070.573653.467636.4563-110.4464
22-0.00170.0148-0.00910.0372-0.00250.0045-0.11120.09480.05340.18860.10310.167-0.128-0.1204-0.00040.3798-0.0491-0.00380.41360.0920.494752.592345.3176-107.0642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 68 )A16 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 135 )A69 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 230 )A136 - 230
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 250 )A231 - 250
5X-RAY DIFFRACTION5chain 'A' and (resid 251 through 279 )A251 - 279
6X-RAY DIFFRACTION6chain 'L' and (resid 16 through 82 )L16 - 82
7X-RAY DIFFRACTION7chain 'L' and (resid 83 through 111 )L83 - 111
8X-RAY DIFFRACTION8chain 'L' and (resid 112 through 149 )L112 - 149
9X-RAY DIFFRACTION9chain 'L' and (resid 150 through 171 )L150 - 171
10X-RAY DIFFRACTION10chain 'L' and (resid 172 through 195 )L172 - 195
11X-RAY DIFFRACTION11chain 'L' and (resid 196 through 232 )L196 - 232
12X-RAY DIFFRACTION12chain 'H' and (resid 4 through 19 )H4 - 19
13X-RAY DIFFRACTION13chain 'H' and (resid 20 through 35 )H20 - 35
14X-RAY DIFFRACTION14chain 'H' and (resid 36 through 47 )H36 - 47
15X-RAY DIFFRACTION15chain 'H' and (resid 48 through 61 )H48 - 61
16X-RAY DIFFRACTION16chain 'H' and (resid 62 through 77 )H62 - 77
17X-RAY DIFFRACTION17chain 'H' and (resid 78 through 92 )H78 - 92
18X-RAY DIFFRACTION18chain 'H' and (resid 93 through 109 )H93 - 109
19X-RAY DIFFRACTION19chain 'H' and (resid 110 through 128 )H110 - 128
20X-RAY DIFFRACTION20chain 'H' and (resid 129 through 154 )H129 - 154
21X-RAY DIFFRACTION21chain 'H' and (resid 155 through 203 )H155 - 203
22X-RAY DIFFRACTION22chain 'H' and (resid 204 through 222 )H204 - 222

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