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- PDB-7o1k: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o1k
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme alpha-E141A, beta-C92A mutant
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / trifunctional enzyme / fatty acid beta oxidation / mycobacterium tuberculosis
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. ...3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsDalwani, S. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland293369 Finland
Academy of Finland289024 Finland
Academy of Finland319194 Finland
Citation
Journal: J.Struct.Biol. / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S. / Lampela, O. / Leprovost, P. / Schmitz, W. / Juffer, A.H. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: ACS Chem Biol / Year: 2013
Title: Structure of Mycobacterial Beta-Oxidation Trifunctional Enzyme Reveals its Altered Assembly and Putative Substrate Channeling Pathway
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionMar 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation_author.name / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
D: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,17940
Polymers240,7524
Non-polymers3,42736
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18080 Å2
ΔGint-338 kcal/mol
Surface area83500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.936, 134.955, 118.930
Angle α, β, γ (deg.)90.000, 110.409, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-630-

HOH

21D-602-

HOH

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase


Mass: 77947.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53872, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein Putative acyltransferase Rv0859


Mass: 42428.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 2 M Ammonium Sulfate, 0.1M Tea pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.86→48.38 Å / Num. obs: 83114 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 53.56 Å2 / CC1/2: 0.986 / Net I/σ(I): 8.4
Reflection shellResolution: 2.86→3.04 Å / Num. unique obs: 4155 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B3H

4b3h


Resolution: 2.86→48.38 Å / SU ML: 0.421 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 2101 2.53 %
Rwork0.1851 80997 -
obs0.1861 83098 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.62 Å2
Refinement stepCycle: LAST / Resolution: 2.86→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16666 0 188 138 16992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002917156
X-RAY DIFFRACTIONf_angle_d0.529523257
X-RAY DIFFRACTIONf_chiral_restr0.04192634
X-RAY DIFFRACTIONf_plane_restr0.00383043
X-RAY DIFFRACTIONf_dihedral_angle_d12.73846248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.930.47111300.36715012X-RAY DIFFRACTION91.14
2.93-30.34711410.31295441X-RAY DIFFRACTION99.31
3-3.080.32321410.29235443X-RAY DIFFRACTION99.13
3.08-3.170.3071410.2645432X-RAY DIFFRACTION99.39
3.17-3.280.29961420.26015465X-RAY DIFFRACTION99.13
3.28-3.390.30761410.25085451X-RAY DIFFRACTION98.9
3.39-3.530.27311380.21325302X-RAY DIFFRACTION96.63
3.53-3.690.21031350.18695230X-RAY DIFFRACTION95.29
3.69-3.890.20881430.1665482X-RAY DIFFRACTION99.54
3.89-4.130.16051410.14595457X-RAY DIFFRACTION99.4
4.13-4.450.16951430.12645502X-RAY DIFFRACTION99.47
4.45-4.890.15111420.12935477X-RAY DIFFRACTION99.1
4.89-5.60.20291370.15375280X-RAY DIFFRACTION95.66
5.6-7.050.20381430.17515540X-RAY DIFFRACTION99.54
7.05-48.380.21430.15215483X-RAY DIFFRACTION97.17
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)
11.32961922219-0.282068975080.1155357065911.530744592840.1330867202141.201378282570.03812082809730.08007512482050.021357995431-0.227448515064-0.04371596752110.327643082253-0.131599290049-0.2670011394520.04380480833280.3670940553710.022606257772-0.085778302640.3831170292020.02265792538150.34341632735-65.283717565850.0125848426-28.4672652292
20.4501574133270.112808901270.4664346507840.9346704125740.5439432219780.974467341608-0.03658390728510.0141038223951-0.01398766252640.0002541010817170.006192074808380.113678682474-0.0566146001831-0.005000909734050.04185793594810.3690316277740.00574967008512-0.02635336354710.3173414923750.04299600375760.355445440306-54.376103717737.766428759-29.3847117101
32.171391686610.736068917142-0.1682059237511.83871649246-0.4756124820761.36039743115-0.04177084102760.132870931229-0.108555731388-0.1238100141490.06759742070770.3611747436860.0726499108884-0.1669350422440.02924173725350.486103216368-0.0602803688285-0.03058952842460.464231924663-0.03202085839470.436207655895-70.781000936613.5701407263-55.8958140069
41.48558939248-0.02429392910240.5568645206171.090850914490.3853574445850.882076062396-0.07159915797460.265413755565-0.124524959918-0.1294578870020.0545487801531-0.04273231180990.06706343959050.0759295895207-0.01006868193650.444935453124-0.07043663338370.04481339604650.409662825346-0.03231661034120.328634554038-44.405623998219.1383711005-52.8521433842
51.784872542250.1290247442020.1498851883161.981507540190.7579830347622.656634498180.134550125387-0.11392720951-0.2040522363750.374494970827-0.09254835043640.05055618037440.0900407158761-0.00160865560824-0.003856696822710.506827683865-0.1306195397940.0135069129060.3857341825130.04477769168450.374721836996-63.67770531088.0798009114930.1242873733
61.156178108350.353049623516-0.427877599961.27010452432-0.07872000979111.05531058167-0.001660261839940.006074898366180.04181941998720.103097884361-0.03242518928160.169226851760.0148090279185-0.1954624907890.01724474982570.369256895684-0.0151398046342-0.01081625796520.3318229559780.00740086643390.303894575569-57.201755320625.545997364423.5749897946
71.49803039178-0.833414644505-0.3286230523511.095611447010.2277573318671.0875296149-0.0550985928233-0.23188602353-0.009200380411290.1872425113570.04140592345210.297720864423-0.0118341644661-0.2053306061890.04371431780670.4393757668420.012216036380.005669708860330.4795399085230.01421076732030.381952191692-56.254160042148.72567592155.1153851283
81.66436028979-0.0794135395076-0.3675732001191.45427391867-0.2645395695421.77800183669-0.0024236861465-0.2128273508110.1441302311270.1114228340210.0512971803826-0.0213184298049-0.2762430111820.1249609957720.01569886299080.375719892525-4.16751827166E-5-0.07443350398310.365333831666-0.03000763505150.264434929306-33.024540020949.078074052245.4250855764
90.9768577842030.101847417760.4441068462751.71986414581-0.1246221290971.601790704890.04604052211150.0330971203313-0.0718928339893-0.009241650202610.0079672919306-0.0334502022430.06876271404480.00100986306676-0.005801562904740.3225039224580.00346712422376-0.02331349478280.2925680702980.003026700538950.258790931732-25.211251688939.9787096558-12.650593773
101.023005419221.310719863990.1705071129142.381535801590.1516405164610.1654497741360.144467684030.118504214102-0.4250404472640.4338310586590.169127305309-0.581686267423-0.004701550176-0.03953408428680.01083011790510.409439094207-0.02151345309620.003267169597070.4108395617790.07348705082990.328848046777-32.878004551947.159787291615.3766972571
110.667212665605-0.04390802616360.3024453501740.4143009504340.7778999143211.98986552809-0.16383406281-0.06375823231720.1781357508790.03623487508610.01362726493610.0340690782034-0.1989424632110.0489487270260.04729305476140.4630530672010.0100288898739-0.04286032314460.3104017447080.05898457073690.387415166668-32.187218493361.0565490582-6.5948416178
120.4899012143310.07607936851080.4166548122960.804895506554-0.2944286255590.6094069073670.0568740942935-0.1347359047930.1314301536170.01919927387610.0488904461960.060330491356-0.2425121614270.0122894479118-0.0007772855379260.30029906309-0.0394185227839-0.02892008550570.330834371590.02810608194130.347127248133-27.392837454250.1337696045.35066956921
131.26975502225-0.509802165126-0.1263063512231.101317737570.1207708407990.876779231757-0.124330916964-0.10388215080.1106054423350.07630923762990.0915045558939-0.18396093509-0.1325233025350.109103899113-0.004527890638650.365149089977-0.0142532737888-0.03249443768520.3640047021350.02796027391650.365368900408-15.837377928652.41690809950.02991025871
140.9155417886250.291185455209-0.3264981062041.046350013490.03281612442341.011636925440.0273894110906-0.0641074743702-0.1603108231940.085310660118-0.00486494134219-0.09038061546360.0693935831638-0.0096931844783-0.01994102295730.3503744551060.0145272921645-0.06060107797330.2814837171970.0460038812220.322125930296-23.776552867825.97632450147.23711480967
150.5831394981740.205272284557-0.5574373417280.351766538519-0.3965410291730.833134797474-0.2580560358730.2103350815370.279044780961-0.1535585517140.236227285968-0.0834519484547-0.04294369656830.0699636294971-0.0009411185625790.357525800596-0.0118485532022-0.03509870743960.324872097281-0.01514308534560.381566211721-27.574455308327.46792431981.53115194671
160.719583420053-1.608870694230.082402221723.637425087990.09632857100530.295567673488-0.0773895561636-0.1363432801520.208554750869-0.1066122450240.191760452492-0.4882031610660.118757378267-0.0177483227971-0.01631274492010.4920935025960.00789268443438-0.02025515850.4589944182970.009359740360870.360798681595-36.019220476319.8697054346-20.7552631544
170.799629278343-0.194481059196-0.02650290359310.7431713560190.3948714649121.235470172440.01197114489740.0367428403723-0.1210220284310.07100289108180.138612064334-0.2171438649860.4523276108950.136751585283-0.0666755891920.443364117971-0.0323686938063-0.07456934496910.3132738721620.05439688860320.425386555429-28.88727731576.380474247445.23804283589
180.9398905426530.434947593380.3549748276450.3274431734070.7270215727542.28068106405-0.07841199244520.0811864590061-0.1616798775640.04863182735730.09220641208350.1022990685040.29436143814-0.309788576242-0.02748079170430.650294402651-0.0344495206001-0.06522518631820.390955763420.005204812876180.60171450989-39.60383690455.08649677065-5.11292669282
190.200701518177-0.0263975086394-0.4102598103590.565034934606-0.03165613700071.146366982050.02168762806080.0498835178667-0.146223758692-0.0373593022590.02599472188740.0311019555240.158453027742-0.112694200983-0.03886287105690.3617964237280.0460374287246-0.03110219755080.3082204887920.03919887227470.332321729553-30.157056159616.1833024536-12.2777681645
201.68286871090.0193451058051.117631719181.407829633990.1127159803562.651532356190.1752325895470.273641283278-0.103658683117-0.2655556294240.0391919658428-0.09974470210830.8413267094010.303005075929-0.05286839846110.502358074733-0.00384768889652-0.02769337916040.4294751478110.02718745071470.458929373775-15.68818392419.8021269156-9.82255671149
211.330699677690.3756063601110.04581563706730.9657471289160.1142807533911.32578282138-0.07205033593630.153456541911-0.2250981076090.05340817703570.045409316453-0.262640372930.322520589830.194878887057-0.04231821227290.4249264863280.0356449512484-0.005176407806160.345350799354-0.0126473915820.509381354816-18.226976084410.9340469692-6.42098786091
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -12 through 211 )AA-12 - 2111 - 222
22chain 'A' and (resid 212 through 326 )AA212 - 326223 - 337
33chain 'A' and (resid 327 through 471 )AA327 - 471338 - 482
44chain 'A' and (resid 472 through 719 )AA472 - 719483 - 730
55chain 'B' and (resid -13 through 59 )BB-13 - 591 - 66
66chain 'B' and (resid 60 through 291 )BB60 - 29167 - 300
77chain 'B' and (resid 292 through 528 )BB292 - 528301 - 539
88chain 'B' and (resid 529 through 720 )BB529 - 720540 - 730
99chain 'C' and (resid 2 through 132 )CC2 - 1321 - 131
1010chain 'C' and (resid 133 through 163 )CC133 - 163132 - 162
1111chain 'C' and (resid 164 through 233 )CC164 - 233163 - 234
1212chain 'C' and (resid 234 through 278 )CC234 - 278235 - 279
1313chain 'C' and (resid 279 through 403 )CC279 - 403280 - 406
1414chain 'D' and (resid 2 through 107 )DD2 - 1071 - 108
1515chain 'D' and (resid 108 through 132 )DD108 - 132109 - 135
1616chain 'D' and (resid 133 through 163 )DD133 - 163136 - 166
1717chain 'D' and (resid 164 through 203 )DD164 - 203167 - 208
1818chain 'D' and (resid 204 through 233 )DD204 - 233209 - 238
1919chain 'D' and (resid 234 through 277 )DD234 - 277239 - 282
2020chain 'D' and (resid 278 through 313 )DD278 - 313283 - 318
2121chain 'D' and (resid 314 through 403 )DD314 - 403319 - 408

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  • 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

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