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- PDB-7ai2: Crystal structure of Se-Met labelled MCE domain of Mce4A from Myc... -

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Basic information

Entry
Database: PDB / ID: 7ai2
TitleCrystal structure of Se-Met labelled MCE domain of Mce4A from Mycobacterium tuberculosis H37Rv
ComponentsMce-family protein Mce4A
KeywordsTRANSPORT PROTEIN / susbtrate binding protein / MCE / Mce4A
Function / homologyVirulence factor Mce protein / Mammalian cell entry, C-terminal / Cholesterol uptake porter CUP1 of Mce4, putative / Mce/MlaD / MlaD protein / membrane / Mce-family protein Mce4A
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.61 Å
AuthorsAsthana, P. / Venkatesan, R.
Funding support Finland, 6items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission713606 Finland
Jane and Aatos Erkko Foundation Finland
Sigrid Juselius Foundation Finland
European Union (EU)653706 Finland
Academy of Finland319194 Finland
European Commission730872 Finland
CitationJournal: Iucrj / Year: 2021
Title: Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis .
Authors: Asthana, P. / Singh, D. / Pedersen, J.S. / Hynonen, M.J. / Sulu, R. / Murthy, A.V. / Laitaoja, M. / Janis, J. / Riley, L.W. / Venkatesan, R.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mce-family protein Mce4A
B: Mce-family protein Mce4A
C: Mce-family protein Mce4A
D: Mce-family protein Mce4A


Theoretical massNumber of molelcules
Total (without water)61,3464
Polymers61,3464
Non-polymers00
Water00
1
A: Mce-family protein Mce4A
B: Mce-family protein Mce4A


Theoretical massNumber of molelcules
Total (without water)30,6732
Polymers30,6732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-48 kcal/mol
Surface area13630 Å2
MethodPISA
2
C: Mce-family protein Mce4A
D: Mce-family protein Mce4A


Theoretical massNumber of molelcules
Total (without water)30,6732
Polymers30,6732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-47 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.022, 134.022, 105.533
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein
Mce-family protein Mce4A


Mass: 15336.584 Da / Num. of mol.: 4 / Mutation: SeMet labelling
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mce4A, Rv3499c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6YC99
Has ligand of interestY

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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: 4.53 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MES, 700 mM ammonium sulfate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 3.6→48.04 Å / Num. obs: 12505 / % possible obs: 99.8 % / Redundancy: 12.41 % / Biso Wilson estimate: 132.91 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 3.6→3.9 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2961 / CC1/2: 0.23 / Rpim(I) all: 1.45 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.61→43.87 Å / SU ML: 0.461 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 32.8121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 654 5.24 %
Rwork0.2165 11822 -
obs0.2183 12476 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.89 Å2
Refinement stepCycle: LAST / Resolution: 3.61→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 0 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223336
X-RAY DIFFRACTIONf_angle_d0.54084520
X-RAY DIFFRACTIONf_chiral_restr0.0481522
X-RAY DIFFRACTIONf_plane_restr0.0041587
X-RAY DIFFRACTIONf_dihedral_angle_d12.7915462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.61-3.890.36271230.30432341X-RAY DIFFRACTION99.48
3.89-4.280.33081220.26962355X-RAY DIFFRACTION100
4.28-4.90.26581260.21562370X-RAY DIFFRACTION99.88
4.9-6.170.24861320.22352363X-RAY DIFFRACTION99.96
6.17-43.870.20451510.18022393X-RAY DIFFRACTION99.96
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)
110.0228171975.439313024845.770526344513.965274470834.351389426085.01682893762-0.7087477843180.2952072074190.55428688447-2.311926655750.3771335052970.740222506515-1.017719987390.097375632920.6557144420681.460696979460.136848291127-0.3011345791410.8993858503050.04824829266520.86376391092250.9720838277-17.6077819632-20.3101562598
26.102993686532.942330376332.066244731875.44236930865-4.181296605066.71220154049-0.225793418931.599680560431.15438921911-0.564142065712-1.0926861089-1.09939142280.2038572203040.1596389620241.32587529611.27916918209-0.00796104188341-0.2306661738211.15140631167-0.1168603057980.63984720481251.284795662-20.597636645-22.2065703492
32.12527220216-0.6114670087980.8217784269523.352977114452.40047720282.476858385511.64648739754-0.456768981110.02896325236111.79228956152-0.919642595232.19106422903-1.57827292102-0.04874236964461.194417071973.61871442195-1.180577354820.3885080622250.614922831356-0.5311215989141.2432745989946.8493720303-33.6245954116-24.4249230117
44.242573292971.457366493781.924318006365.660848489261.428021957610.9334477591040.7366338103690.31032949590.6960609503044.40207379862-0.690394031721-0.5333804278741.838813741770.92886133075-0.08675226805671.68029284572-0.0328841648113-0.02480549372631.233686542350.3222525344140.82642215498556.6130109459-21.2250798198-11.9801617806
54.478510700165.7418972004-0.01140969955899.31264690486-1.951141882985.303496584421.03911042805-0.659779342766-0.30230272303-0.138626758639-1.54123741935-0.609421480187-0.1910238854381.152812915790.5476389280591.41203286633-0.04101484157950.08972140875740.9843367384560.2159392445021.0773006312470.361144092811.2991310505-13.2435664337
62.002119149012.16824552435-8.633941751373.80636341151-4.343750653068.85258647582-0.786058303182-0.230710997746.41003874032.805060068532.252650662910.539702705645-2.23721362325-1.63432006226-0.7434725171532.579444714280.566044879242-0.1665045616081.054971778510.1074381617711.257202858757.82497523212.78476975717-4.53309574618
71.954664787271.873483591242.033228470598.832462108584.355410060511.98369631148-5.387674935882.740009085381.66247387105-4.022336590681.266532408781.071176744760.17308663956-0.650447001739-2.567583641851.48023583702-0.2669519934240.1251758534031.036125446780.07127099559061.1080004806169.201814309612.578452488-30.8842842089
83.866462891324.595589119013.757258263965.417561907314.485551244533.73789441711-0.8744513392290.611972147333-2.15288586012-0.8002122712882.117833572111.47523036084-3.55681503598-0.286676664974-0.995642302381.109048008280.1940815327610.0903914448740.7721595722340.3046534194051.139219383563.0933275785-2.65268889494-15.3287218866
95.1102021527-2.85836722098-1.231437465118.684508437934.048677545378.07320170007-0.93979831771-0.987875994309-0.528709333166-1.482790132650.7369887099370.5523774110890.4453599312420.1095277019460.2388999517521.581027527230.09936652113510.1179302034481.023503183760.167806371450.94785750111761.86655806818.32364104355-19.0811670347
106.821265008494.96696958625-3.179572343948.722605098992.380228994095.99916415818-0.5495650928240.0291275593183-0.799901053231-0.953692150211-1.0041425124-4.70671344940.1241113763351.219567731061.351253361761.385426123080.1522705396580.2517778996630.9686984437720.07391929390821.3184823729270.33765749081.62857973731-20.8377002851
115.131815719910.117062278703-0.05599755024474.63566557526-2.478738555052.859711437060.0526856275425-0.5424053128440.676317846836-0.600059588814-0.773630240251-0.6923122893770.2430315022110.636149460.5902664082281.35612310179-0.2277742702040.1287430549561.148575519160.100812033950.64595328498965.804650917811.1086603577-14.0020322858
127.779615200245.17806991011-2.617205398666.417949578822.596840197497.016554002952.59947780478-1.09134969251-1.165428082931.09655528077-2.04223300747-2.775746756351.744608122591.75551701417-0.2080915454431.292118793890.599377616132-0.2229839987351.415276725270.2274375393041.0307218173756.0705480219-23.8945543458-15.7717825335
135.697283538472.250450326222.422691395439.229498903744.337301855872.39076580368-0.180318342051-0.26116246774-1.41922350425-2.297567873070.5563752944822.75283703642.17890019165-1.59846753281-1.312772230433.46608206684-2.314996756230.849365273086-0.074926860511-0.8046526398072.5255819083345.2171392843-38.3134458862-12.3350932295
144.83284156795-2.456345990991.720960223644.87231752619-5.835871924967.38143552479-0.276790626985-1.71536103421-0.0597855367351-0.322166949372-4.826735395170.558660171562.60014849359-0.8695577657873.800048277131.1667003172-0.3182802792950.3206600547441.57885825861-0.3308137208681.5746516261541.8237530671-27.8262544525-19.3909510321
152.00751307989-4.774363849961.25790447652.765286125760.146506639283.79978249976-1.940191964621.02482042598-3.346322973191.332498832910.579323869927-0.8029352920450.926787086584-0.9258033676760.8637643424961.62487616621-0.1740350754040.3207008910880.5859683082030.2467400634661.2780528304460.7846511833-22.5622459265-9.16227192802
161.996509037680.765774390859-3.54115411663.06019317543-4.00778614186.83010944648-1.53169494840.535074762552.19173567685-0.4788366010310.569224211181-5.23984974749-1.78235427312-1.521565049511.192543058762.677180239750.00349432027879-0.2529673774210.7485017244390.181300066831.6202695681479.37881714143.4351424625233.1093060671
177.622155921974.412990438833.295143882599.281020738853.871297231277.687315916430.921254829390.244737680931-0.7248636143841.81251720777-1.17907766166-0.647273927936-0.2971219168960.08079921494710.4201185420271.703117503810.231834361063-0.3037988078231.28992741998-0.1507273885251.0090473696864.27143999930.98382414307111.6572408664
185.284328305310.4821304646385.843494792339.18453831572.712505648287.40259757919-0.1255867913351.60578685486-0.04607764644990.448209140618-0.7920791584880.539510409924-0.94192922606-0.7678304790811.072239350891.773528421510.2019177596650.08122410481851.72043044524-0.1490184666910.94493293508360.8232408262-0.50018813337115.2645289122
198.621331326770.4931154667893.313552717079.50408316126.860846994335.57985374590.953534637988-1.009678622920.6902901765470.47454007108-0.689297630723-2.25384819292-2.04090859988-0.653907223323-0.1926578795773.092425219460.10216607341-0.4942430837071.08515392840.0974402797541.2007852911866.00312368117.638343478999.99026423987
209.154715806591.15358554378-4.14425508666.95211347126-0.6410820536727.871142230220.993124819222-1.78742244718-0.5028423396170.700838689997-1.02496699509-0.7226056173511.10468815246-0.0308259923272-0.03374909081381.1025229265-0.115936579671-0.2069088830250.87809922980.2821123001810.70987741202761.5767796121-35.0518715151.99132921189
217.52823300236-2.288202228784.087229834564.39969530733-2.512017944746.66360958944-1.564641168581.04049610457-4.17489832019-2.338402653060.465022404982.49405799891.21934212393-2.313031929290.4874709206021.38938875548-0.4466288686990.05310705608871.31977953841-0.3172866129821.4445874688853.4384011769-21.5170161554-3.013882413
223.74822186254-2.48201551591-3.35776067346.091712417813.369544570043.586402192630.715099364264-5.36637316972-0.0337539867332.20350176578-0.991045852040.1494136247242.247881676882.653589698670.2895328956871.52900074236-0.0610731750446-0.4220994705382.252119391740.1552308543730.85806760170764.2765633189-34.140929467813.0190532005
232.121770340412.750579633591.406805379833.359323915431.03105361345.924834439441.31000325881-1.50271938055-0.1391099926031.81813353966-1.129514835440.13155526699-0.915282147827-0.851373987603-0.2054458080691.09420693545-0.09305959996290.2575607740381.110034823120.005332548525160.74508733295157.395610066-26.33442205466.54422237787
249.76170760007-1.923110881516.161955362835.26029188482.518044675938.863944982521.14434055992-0.79221027351-0.3516804384141.21930124538-1.05252924682-1.702496811830.988856730174-0.4197349002110.005779258781820.81243295483-0.0570679246781-0.05157200426841.17515136409-0.05894401346040.8930835249464.6816313906-28.794421135710.4086672581
258.82359713992-2.10059088373-3.282448149344.51890095756-0.205270085468.746535870251.26627684363-0.632691143759-1.35417453721-1.48418776361-1.755313234830.9883304609560.642512824173-1.735016147330.3900464303470.826347726579-0.233013989856-0.1688626647460.954256098270.1309583022120.68230779323457.9881013087-30.21201487211.35072174814
265.679857441452.90952119826-1.536824152634.079040013213.286149464176.54104697653-0.579428996074-1.99772081157-0.261082566555-2.32390219167-0.120547502701-1.2347640427-1.735359030811.692292995810.2497438480891.472254447480.255636423618-0.3651128361180.882951348240.08623887771620.99627766801267.14159816762.613157713876.22599044562
277.276216958711.063420268273.228403331345.8108346555-4.535851189087.26582397768-3.439833567520.4379956984941.286039257973.62270385142-0.2655557745020.126993059734-1.014430257091.046018874382.895287828324.07200922036-0.368418770228-0.3221210540291.29423778030.1015369570191.8710384851264.030799080120.99371405055.96437453489
286.741161431821.63729495118-1.381894918398.625235837517.643511715238.05137771884-1.323284722770.2810842437132.13472668085-0.4257502694771.78026681691-1.28330208629-4.14336927645-0.1318936170550.5102079542424.239464834370.78989031106-0.9657044169291.47880447913-0.346483766591.0051584620358.223058376912.475731266814.5128702158
292.00091556794-4.53096831715-7.687629149074.589158615811.489721013856.3773132482-0.697970785877-1.63489304054.287900139130.08950932333120.0853900260608-3.08816250561-1.836115368740.978615108110.3948794280432.036240255370.0671591519117-0.1770664558041.025530938260.2426288017451.5855241800667.4085672311-0.0771537737534-1.15274597985
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 39 through 58 )AA39 - 581 - 20
22chain 'A' and (resid 59 through 87 )AA59 - 8721 - 49
33chain 'A' and (resid 88 through 97 )AA88 - 9750 - 59
44chain 'A' and (resid 98 through 107 )AA98 - 10760 - 69
55chain 'A' and (resid 108 through 136 )AA108 - 13670 - 98
66chain 'A' and (resid 137 through 145 )AA137 - 14599 - 107
77chain 'B' and (resid 32 through 46 )BB32 - 461 - 15
88chain 'B' and (resid 47 through 58 )BB47 - 5816 - 27
99chain 'B' and (resid 59 through 75 )BB59 - 7528 - 44
1010chain 'B' and (resid 76 through 87 )BB76 - 8745 - 56
1111chain 'B' and (resid 88 through 107 )BB88 - 10757 - 76
1212chain 'B' and (resid 108 through 117 )BB108 - 11777 - 86
1313chain 'B' and (resid 118 through 122 )BB118 - 12287 - 91
1414chain 'B' and (resid 123 through 136 )BB123 - 13692 - 105
1515chain 'B' and (resid 137 through 144 )BB137 - 144106 - 113
1616chain 'C' and (resid 32 through 39 )CC32 - 391 - 8
1717chain 'C' and (resid 40 through 64 )CC40 - 649 - 33
1818chain 'C' and (resid 65 through 87 )CC65 - 8734 - 56
1919chain 'C' and (resid 88 through 107 )CC88 - 10757 - 76
2020chain 'C' and (resid 108 through 136 )CC108 - 13677 - 105
2121chain 'C' and (resid 137 through 144 )CC137 - 144106 - 113
2222chain 'D' and (resid 38 through 46 )DD38 - 461 - 9
2323chain 'D' and (resid 47 through 67 )DD47 - 6710 - 30
2424chain 'D' and (resid 68 through 92 )DD68 - 9231 - 55
2525chain 'D' and (resid 93 through 107 )DD93 - 10756 - 70
2626chain 'D' and (resid 108 through 117 )DD108 - 11771 - 80
2727chain 'D' and (resid 118 through 122 )DD118 - 12281 - 85
2828chain 'D' and (resid 123 through 136 )DD123 - 13686 - 99
2929chain 'D' and (resid 137 through 144 )DD137 - 144100 - 107

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