[English] 日本語
Yorodumi
- PDB-6mlk: Structure of Thioesterase from DEBS with a thioesterase-specific ... -

+
Open data


ID or keywords:

Loading...

-
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


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / 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 / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / 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
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Chloride


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more