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- PDB-7ai3: Crystal structure of MCE domain of Mce4A from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 7ai3
TitleCrystal structure of MCE domain of Mce4A from Mycobacterium tuberculosis H37Rv
ComponentsMce-family protein Mce4A
KeywordsTRANSPORT PROTEIN / substrate 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.2May 1, 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: 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)60,4084
Polymers60,4084
Non-polymers00
Water25214
1
A: Mce-family protein Mce4A
B: Mce-family protein Mce4A


Theoretical massNumber of molelcules
Total (without water)30,2042
Polymers30,2042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-42 kcal/mol
Surface area13500 Å2
MethodPISA
2
C: Mce-family protein Mce4A
D: Mce-family protein Mce4A


Theoretical massNumber of molelcules
Total (without water)30,2042
Polymers30,2042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-43 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.202, 131.202, 105.576
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: 15102.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mce4A, Rv3499c / Plasmid: pETM 11 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I6YC99
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Sodium HEPES, 100 mM LiCl2, 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2019
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.9→47.8 Å / Num. obs: 23016 / % possible obs: 100 % / Redundancy: 15.43 % / Biso Wilson estimate: 66.3 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3 Å / Redundancy: 15.57 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3714 / CC1/2: 0.43 / Rpim(I) all: 0.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet labelled Mce4A

Resolution: 2.9→42.95 Å / SU ML: 0.4652 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 28.4659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1128 4.91 %
Rwork0.1947 21840 -
obs0.1966 22968 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.22 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 14 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143342
X-RAY DIFFRACTIONf_angle_d0.41374530
X-RAY DIFFRACTIONf_chiral_restr0.0459523
X-RAY DIFFRACTIONf_plane_restr0.0031589
X-RAY DIFFRACTIONf_dihedral_angle_d16.79131244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.36751590.32312695X-RAY DIFFRACTION100
3.03-3.190.37721380.30192727X-RAY DIFFRACTION100
3.19-3.390.34451310.27752715X-RAY DIFFRACTION99.89
3.39-3.650.27761330.23322743X-RAY DIFFRACTION99.79
3.65-4.020.24191040.21022741X-RAY DIFFRACTION99.96
4.02-4.60.18491360.1632734X-RAY DIFFRACTION99.93
4.6-5.790.19611680.16012718X-RAY DIFFRACTION99.97
5.8-42.950.20821590.15782767X-RAY DIFFRACTION99.76
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)
14.67678225216-3.769025587550.1075064221953.355364770811.159678473635.767251532990.3823895714590.9379432214330.727555089856-0.675553527711-0.1122335937890.3931227511780.242540834044-1.03351598883-0.3838580464550.501434315186-0.125635074019-0.02386309086040.8664936987110.2256956979370.605074772292-0.54781624548669.923057736561.6052383838
25.06644376445-4.17585716851-4.260209947434.619283835611.289899412227.75463999364-0.951700481607-1.405007806280.08242529700550.19632676180.32279086334-0.5347488437150.7465514602530.8817102486990.857881903410.685014589760.1931234392470.05084104924740.6188516462090.09275861480370.40612722481126.420642703456.354273604664.1058715192
35.795284773940.920430540633-4.947511915310.19582733175-0.7338962677834.275910837671.873005586922.30841549279-1.86153892101-1.683672969210.17012397297-0.3313008606382.175621431872.83219415539-1.667231659831.34804497860.531835114727-0.3310861809551.99046421919-0.03707870362981.2643384357448.849763978345.256830010863.4363870586
41.997655479263.002868123920.726800454461.995586013733.931597151891.482372686350.5748875144930.424905292113-0.901927605452-0.403604201611.34489265659-2.00319090531.331541869463.102154045041.042638583951.762667387741.117114513270.3394734686332.354847989-0.02206337039770.97842908313747.481180360642.749365985452.5654395687
59.125741521974.33366250009-5.095913768245.26134180546-2.675201494673.78968395056-0.864382063085-0.207568268746-2.3725011875-0.226813090070.652088867064-0.9066755848953.48759678246-0.2191979202750.341192391161.454531762990.3282597565580.3237798617671.161864734850.1276386459160.86381539010135.709745546443.303322315555.0391393342
65.705594190466.198091677125.81330333426.877829547656.427635918545.9999332325-1.334899157660.1941606286641.45781710823-1.616799329510.167218766675-0.0100691665097-1.586236676650.9903106472741.084011615660.9338723262160.272017423316-0.1532158180151.027076926350.2088007940530.99170093510333.068481107357.380095330869.7525412591
74.598669981670.240549385792-1.392490484216.37387664245-0.6516849119497.14506118864-0.39462160486-1.03808923564-0.8929425397640.625234597668-0.0254811547477-0.1040949949960.9076154161750.4655659420860.4647356927520.8073839142950.1246535218890.1388941424870.7303897943360.06096258436980.5913698273295.8797016182553.26743383689.7316180937
84.95794335884-3.34151034285-0.1538723832013.135940081310.6294910806183.63830308493-0.3144742346760.3561841273290.604342839203-0.1048489522320.13645527624-0.462162556391-0.07025779266440.3719806379580.1545968694860.6010358984020.121205214960.032116019230.7571580695830.08458607304250.52563198393938.910305355553.455662811479.4387109682
93.323599911093.87786314562.522564267338.755986758666.18193619224.375115710921.46202478695-0.1217969229311.32845509824-0.0818973321989-1.616725783852.725714727473.08933164177-2.35422547178-0.3237952428991.37782553962-0.137779092777-0.2075592586121.930197796960.06715524905671.2620792907547.408272118850.5671422069106.023668415
106.03643302072-0.920233153246-4.465867143887.141029993741.785735842948.42186921448-0.451992137625-1.535657748640.07744712890640.3749258373330.673135307785-0.1811849358180.352087771653-0.229093651591-0.002234423706460.7397254902550.230160414801-0.07732897504540.783125919347-0.01759908167220.53078845174435.915490843152.264045215785.6693895035
115.57520049466-1.74761543017-1.430901364241.015986015292.021452123125.81608729344-0.179204057458-1.211004229741.504572788690.137314099913-0.109761662813-0.952318219688-0.609973520395-0.171449021130.3520106885870.7254587249310.305883230576-0.04320983736031.0695467382-0.1635299924950.75818789147133.911673772454.492789912189.6104117536
124.677759773831.34682587687-0.9322234726286.52637464514-1.532104168168.66888729447-0.6231436271-0.8176528149190.6510401773350.3506737567560.162406863369-0.798388068614-0.1297080043630.6770684487450.5429933087290.7623330435090.361963952074-0.1561453386561.00565547344-0.1084335554220.66021719661943.756546038652.809387413187.0310174383
133.12954814346-1.70293160057-0.09217703561.08343087871-0.3677019120182.05528408463-0.2870983338870.6975310959080.0460208808973-0.1959773776220.01696083027520.1688219288110.111656922038-0.4217671933540.3771015995150.636543034685-0.02057874836560.02855761537750.634958881945-0.04533794803040.4710603906674.9423795262155.489169557283.4694719206
145.66863890332-1.78894169826-2.409161944177.11241468433-4.279780423667.09828634267-0.1396150262581.04685215088-0.4284348334971.07076905767-0.0597531583730.06773952391590.236952277376-0.2341719947560.4489204528050.7443615518990.071879486296-0.02277651243930.654014397197-0.06766347874390.5417184592595.1465902298654.726841741682.0678444751
155.78853021944-2.989337487970.07251120074272.254711922352.148482354286.665160083540.0725814497225-1.315661431223.225734244840.9280535487170.260134986037-2.17058415425-0.09896113635870.112924447155-0.05103338793480.8044893287870.3617512852930.009898042321911.44278679447-0.1466379128021.4573399708141.906257517666.115421622635.5573712956
164.92570070757-0.165481599096-0.3338703314626.348920327842.282084223426.940219303880.0866329897171.284160968980.455138218779-0.261132601068-0.534572949830.4797477409490.438810686264-0.4409720161310.5115339429490.8762790121150.2152610227080.1262350318631.030798677370.1092561500840.56988319726730.949717235453.393140120455.9740414139
179.07525880954-2.89507571968-2.07941187492.276976097030.1076644176713.3686353689-0.4766413432640.438976766804-0.02058590145330.122835906550.0315967047964-0.26908063510.6406304390780.4077032767170.444757241260.7254799069650.007900380813960.003883482918090.729281045201-0.009705150069080.4245340989521.170556886958.391366701360.9016432098
186.80306443599-1.41906107331-0.2701533829144.46543313811-5.795159551978.2798783366-0.6573028809880.214893821780.0464898720976-0.6492464564080.458323848887-0.2944970574820.274936543556-0.6632463427210.1634303556140.528163051142-0.1377623868850.02577552742140.684717017347-0.1074390886830.5058046661315.9787318415766.01042412768.3458508005
199.47490582984-2.113724888080.01831876626298.32969740184-2.143294230423.457341413590.3646396025291.474355356650.210555617607-0.664437512426-0.0641127447391-0.2325961334940.4145579587950.129947001136-0.3461624041840.557097002863-0.02082489960050.01574542802270.856832512060.001093387766680.5396500677759.0384650286266.993014782160.0761127662
209.513353503324.28770375498-8.113265350258.34672070209-1.192847061727.89629289391-0.1655814765020.933925385975-0.637147953611-0.28694378286-0.0981853638937-0.9068785748690.686802879907-0.5801341660120.2794679093670.6799088989820.086329843472-0.1389584373870.6853423060990.2102279167510.5154709490516.0515820260165.892237347660.0382698968
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 80 through 101 )DD80 - 10143 - 64
22chain 'D' and (resid 102 through 116 )DD102 - 11665 - 79
33chain 'D' and (resid 117 through 121 )DD117 - 12180 - 84
44chain 'D' and (resid 122 through 126 )DD122 - 12685 - 89
55chain 'D' and (resid 127 through 136 )DD127 - 13690 - 99
66chain 'D' and (resid 137 through 144 )DD137 - 144100 - 107
77chain 'A' and (resid 39 through 103 )AA39 - 1031 - 65
88chain 'A' and (resid 104 through 145 )AA104 - 14566 - 107
99chain 'B' and (resid 32 through 39 )BB32 - 391 - 8
1010chain 'B' and (resid 40 through 64 )BB40 - 649 - 33
1111chain 'B' and (resid 65 through 78 )BB65 - 7834 - 47
1212chain 'B' and (resid 79 through 101 )BB79 - 10148 - 72
1313chain 'B' and (resid 102 through 126 )BB102 - 12673 - 97
1414chain 'B' and (resid 127 through 144 )BB127 - 14498 - 115
1515chain 'C' and (resid 32 through 39 )CC32 - 391 - 8
1616chain 'C' and (resid 40 through 79 )CC40 - 799 - 48
1717chain 'C' and (resid 80 through 126 )CC80 - 12649 - 95
1818chain 'C' and (resid 127 through 144 )CC127 - 14496 - 113
1919chain 'D' and (resid 38 through 58 )DD38 - 581 - 21
2020chain 'D' and (resid 59 through 79 )DD59 - 7922 - 42

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