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- PDB-3qf4: Crystal structure of a heterodimeric ABC transporter in its inwar... -

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Basic information

Entry
Database: PDB / ID: 3qf4
TitleCrystal structure of a heterodimeric ABC transporter in its inward-facing conformation
Components
  • ABC transporter, ATP-binding protein
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsTRANSPORT PROTEIN / multidrug transporter
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ABC transporter, ATP-binding protein / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHohl, M. / Briand, C. / Gruetter, M.G. / Seeger, M.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation
Authors: Hohl, M. / Briand, C. / Grutter, M.G. / Seeger, M.A.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3814
Polymers132,8512
Non-polymers5312
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-93 kcal/mol
Surface area51360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.330, 84.310, 115.780
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ABC transporter, ATP-binding protein / ABC transporter TM287


Mass: 65060.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0287 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC3
#2: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288 / ABC transporter TM288


Mass: 67789.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2010 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 46481 / Num. obs: 46251 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.14
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.54 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXDphasing
SHELXEmodel building
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→24.927 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7035 / SU ML: 0.48 / σ(F): 1.99 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 2312 5.01 %Random
Rwork0.217 ---
obs0.2193 46149 99.28 %-
all-46481 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.536 Å2 / ksol: 0.269 e/Å3
Displacement parametersBiso max: 271.21 Å2 / Biso mean: 118.1531 Å2 / Biso min: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.7027 Å20 Å238.6133 Å2
2---5.1601 Å20 Å2
3---5.8628 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9166 0 32 4 9202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039355
X-RAY DIFFRACTIONf_angle_d0.72812657
X-RAY DIFFRACTIONf_dihedral_angle_d13.4283509
X-RAY DIFFRACTIONf_chiral_restr0.051501
X-RAY DIFFRACTIONf_plane_restr0.0021590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-2.95920.47621330.368252099
2.9592-3.02340.41941360.3374257399
3.0234-3.09360.34711340.3146254699
3.0936-3.17080.39641340.28162551100
3.1708-3.25640.38921370.26842589100
3.2564-3.3520.32091350.2613256999
3.352-3.45990.34451360.2324255999
3.4599-3.58320.28941360.2204257799
3.5832-3.72620.25351340.2265255499
3.7262-3.89520.31921360.21912574100
3.8952-4.09970.24821360.20552584100
4.0997-4.35530.23711370.19022590100
4.3553-4.68960.22421350.173256399
4.6896-5.15770.23081370.16472598100
5.1577-5.89540.22651370.21112611100
5.8954-7.39530.29571380.2412614100
7.3953-24.92820.20521410.2065266599
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)
12.9279-0.9592-1.46411.23990.2372.01150.1011-0.15640.4225-0.08950.11190.0102-0.17240.2176-0.1260.4418-0.12370.02410.2323-0.11050.4757-29.127617.409833.1918
23.55030.8031-1.56910.6777-0.49831.69420.34011.41661.28460.07780.01220.33830.0319-0.5485-0.10290.686-0.17190.25270.8206-0.0580.7856-44.0419.56413.9077
31.4877-0.5013-1.90950.7126-0.00441.88960.5383-0.53910.6151-0.04110.0723-0.2221-0.59880.3538-0.33550.7667-0.17270.31930.4801-0.04020.8342-60.497928.34751.1554
43.1912-0.1348-0.34760.7890.1085.2035-0.75051.23380.4178-0.88660.1594-0.0658-1.3889-0.0746-0.41292.3549-0.83180.78381.4463-0.34591.3089-74.808431.428142.2227
51.3822-0.4148-0.5930.27860.18822.29410.1627-0.35170.62490.48610.0723-0.0077-0.5123-0.7213-0.35690.57120.0150.16120.46260.00680.8405-75.686827.12260.1201
62.6186-0.5045-0.67161.6761-0.36511.97510.08990.3462-0.5585-0.0163-0.1462-0.35710.38360.00590.11360.74980.01540.26390.3139-0.02980.7343-67.5984.228563.3402
71.09050.49940.75931.7521.19924.7372-0.21520.6144-1.1804-0.017-0.414-0.0509-0.3146-1.51580.3461.6629-0.4370.23511.00480.08780.8468-82.14435.596165.2443
83.41830.7322-0.31741.7584-0.22521.2709-0.27030.6723-0.4445-0.0751-0.20170.88120.6273-0.6820.20070.45180.0828-0.02180.84880.00351.058-92.357219.537457.3233
91.6677-0.3379-0.7843.03630.32570.7061-0.24830.5201-0.54110.0421-0.0954-0.22480.16380.16030.1590.7324-0.30570.22060.8287-0.27360.2993-31.9401-4.67147.6282
101.06080.302-0.75041.8180.76860.8428-0.46820.05930.14090.03910.2459-0.05050.2925-0.63550.17180.8118-0.23370.12741.096-0.13430.7298-57.832-6.503522.2728
111.7312-0.2588-1.29370.7240.0271.6872-0.3294-0.0532-0.49070.1702-0.09450.22040.39050.1010.09990.4513-0.00410.07880.2656-0.05840.4868-30.36472.071433.9803
120.7444-0.5456-0.20370.29710.41770.87330.1814-1.6145-0.1067-0.0856-0.47680.1299-0.0528-0.27980.07871.0325-0.39280.34550.8856-0.23171.4753-54.2221-12.187424.123
132.66230.2256-2.4941.7993-0.43034.4709-1.04660.5375-1.17830.774-0.1196-0.18322.25540.42040.81360.5616-0.60860.41760.756-0.44881.156-88.3348-16.07238.6986
142.49450.1105-2.44213.3423-0.67733.07630.77331.30161.6187-0.9869-0.57820.768-1.5021-0.5701-0.13190.9423-0.2158-0.02161.9861-0.08531.2014-86.11810.296925.5136
151.1611-0.18530.35180.2596-0.47161.0037-0.9881.24790.48710.79820.98030.4730.9378-0.54380.47080.6213-0.26380.05411.2-0.10090.7231-91.48836.499335.7863
160.8688-0.0501-1.06681.71481.24972.208-0.36630.199-0.66850.56810.02151.06720.196-0.71340.27310.9567-0.52420.29461.3167-0.21961.2075-98.0733-3.88151.6095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -2:159)A-2 - 159
2X-RAY DIFFRACTION2(chain A and resid 160:293)A160 - 293
3X-RAY DIFFRACTION3(chain A and resid 294:339)A294 - 339
4X-RAY DIFFRACTION4(chain A and resid 340:346)A340 - 346
5X-RAY DIFFRACTION5(chain A and resid 347:413)A347 - 413
6X-RAY DIFFRACTION6(chain A and resid 414:495)A414 - 495
7X-RAY DIFFRACTION7(chain A and resid 496:517)A496 - 517
8X-RAY DIFFRACTION8(chain A and resid 518:569)A518 - 569
9X-RAY DIFFRACTION9(chain B and resid 10:96)B10 - 96
10X-RAY DIFFRACTION10(chain B and resid 97:157)B97 - 157
11X-RAY DIFFRACTION11(chain B and resid 158:301)B158 - 301
12X-RAY DIFFRACTION12(chain B and resid 302:351)B302 - 351
13X-RAY DIFFRACTION13(chain B and resid 352:431)B352 - 431
14X-RAY DIFFRACTION14(chain B and resid 432:491)B432 - 491
15X-RAY DIFFRACTION15(chain B and resid 492:536)B492 - 536
16X-RAY DIFFRACTION16(chain B and resid 537:597)B537 - 597

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