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- PDB-4q4a: Improved model of AMP-PNP bound TM287/288 -

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Basic information

Entry
Database: PDB / ID: 4q4a
TitleImproved model of AMP-PNP bound TM287/288
Components
  • ABC transporter
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsHYDROLASE/TRANSPORT PROTEIN / ABC exporter / Multidrug transport / ABC Transporter / Membrane Transporter / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / 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: 2.6 Å
AuthorsHohl, M. / Gruetter, M.G. / Seeger, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.
Authors: Hohl, M. / Hurlimann, L.M. / Bohm, S. / Schoppe, J. / Grutter, M.G. / Bordignon, E. / Seeger, M.A.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 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_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_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_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
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,3814
Polymers132,8512
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-93 kcal/mol
Surface area51070 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 / ABC transporter / ATP-binding protein / Lipid A export ATP-binding/permease protein MsbA


Mass: 65060.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287, THEMA_03290, Tmari_0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC3
#2: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 67789.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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

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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 / 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, 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
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 64231 / Num. obs: 63492 / % possible obs: 98.85 %

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Processing

Software
NameVersionClassification
SHELXDphasing
SHELXEmodel building
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→24.927 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 40.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 3181 5.01 %Random
Rwork0.2257 ---
obs0.2278 63492 98.85 %-
all-64231 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→24.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9134 0 32 0 9166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049323
X-RAY DIFFRACTIONf_angle_d0.85812614
X-RAY DIFFRACTIONf_dihedral_angle_d14.7223496
X-RAY DIFFRACTIONf_chiral_restr0.0591495
X-RAY DIFFRACTIONf_plane_restr0.0041585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63880.49351310.47592499X-RAY DIFFRACTION94
2.6388-2.680.47171330.43722508X-RAY DIFFRACTION97
2.68-2.72390.53031370.41992593X-RAY DIFFRACTION98
2.7239-2.77080.47281350.40322573X-RAY DIFFRACTION98
2.7708-2.82110.41871390.36572624X-RAY DIFFRACTION98
2.8211-2.87530.43911350.34042558X-RAY DIFFRACTION99
2.8753-2.93390.42961370.32652598X-RAY DIFFRACTION99
2.9339-2.99760.37541380.3032621X-RAY DIFFRACTION99
2.9976-3.06720.37521370.2982603X-RAY DIFFRACTION99
3.0672-3.14370.35181400.27812646X-RAY DIFFRACTION99
3.1437-3.22850.34331390.27112635X-RAY DIFFRACTION99
3.2285-3.32330.37191390.24922638X-RAY DIFFRACTION99
3.3233-3.43030.31841380.24322618X-RAY DIFFRACTION99
3.4303-3.55260.29051390.21872625X-RAY DIFFRACTION99
3.5526-3.69440.2341390.21972642X-RAY DIFFRACTION100
3.6944-3.8620.28911420.21112685X-RAY DIFFRACTION100
3.862-4.06480.24871370.1942593X-RAY DIFFRACTION100
4.0648-4.31820.22051390.18562650X-RAY DIFFRACTION99
4.3182-4.64960.21281420.17022686X-RAY DIFFRACTION100
4.6496-5.11390.23591390.1742632X-RAY DIFFRACTION100
5.1139-5.84560.24121400.21392664X-RAY DIFFRACTION100
5.8456-7.33360.25321420.24242699X-RAY DIFFRACTION100
7.3336-24.92840.21381440.20882721X-RAY DIFFRACTION99
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)
13.4265-1.0308-1.18021.60310.28442.6020.0625-0.22660.3358-0.19950.1115-0.1235-0.08910.4341-0.23750.6691-0.14780.00550.3988-0.08970.7142-29.082217.541232.4904
29.2113.5456-3.41751.3378-1.38861.95490.15521.71110.8634-0.01020.02950.50280.1059-0.9803-0.12271.0533-0.18840.06451.5071-0.06091.065-56.13956.448916.1284
37.8441-3.188-3.80374.69782.27036.13150.46450.98360.9339-0.13040.02220.0929-0.282-0.1239-0.47661.0038-0.06240.16661.0080.08321.024-22.319215.788212.3089
43.927-1.2032-2.82390.93490.64582.59050.26260.38720.4375-0.1261-0.01360.0856-0.3419-0.4614-0.28151.1689-0.12410.19360.9661-0.04041.1764-68.057130.424153.2665
55.86452.4410.31673.98870.05453.21410.02910.43110.72680.30810.07420.5239-0.2444-0.5541-0.0720.890.0970.0990.91370.04131.0811-74.822126.24960.7707
64.1777-0.09740.11446.3725-0.22122.1323-0.05920.0863-0.44250.0252-0.076-0.32770.50470.19330.05451.24130.02020.20080.78750.03461.1696-66.92513.510763.8235
77.45822.9453-3.20876.3305-2.79197.1194-0.22330.0283-1.62380.24460.39720.59761.0912-1.8344-0.08051.3563-0.14770.14441.13920.14261.3484-81.29139.074664.675
84.33881.24650.84794.8701-0.35224.2889-0.05160.79280.3385-0.6613-0.38340.6515-0.084-1.48490.33890.86060.00940.03261.3989-0.07551.4127-93.935319.614256.2582
92.21092.90013.05543.84264.01684.22330.17680.1935-0.37521.1587-0.3078-0.65051.4078-0.63020.13461.5857-0.33260.50490.9708-0.21811.5165-47.0311-16.721127.2653
100.8209-0.98960.47622.81190.16320.6236-0.25931.1719-0.2493-0.7488-0.0678-0.61410.1853-0.34180.28271.4605-0.27770.33031.6541-0.41010.8321-27.1511-3.09113.0062
113.21230.4642-0.95150.9171-0.08581.4373-0.27010.7422-0.4746-0.18670.0955-0.00020.3453-0.39170.18230.9772-0.20360.01561.047-0.23420.7672-45.3543-5.279916.03
124.1454-0.8717-2.71830.95260.00832.2992-0.477-0.2973-0.44340.30950.14450.19130.49350.23870.34850.9038-0.01630.07050.7542-0.06970.96-33.66134.420439.8534
135.63130.13430.07210.00310.11611.29410.5353-0.6611-0.52070.0697-0.48550.27820.4036-0.3833-0.01821.3926-0.31590.28861.1693-0.24241.5984-46.8782-10.338721.947
143.1452-0.0705-2.45461.23250.3872.1159-0.41370.8809-0.8722-0.1749-0.01060.57470.8134-0.76790.30850.956-0.49890.00541.5212-0.35831.2665-87.9613-5.679133.1695
152.4802-0.1778-1.40173.7212-1.10351.8549-0.00010.5244-0.27810.36020.08130.61370.613-0.69960.03761.1373-0.26720.02931.7097-0.21471.2735-92.22982.307739.2004
163.4643-1.64740.04933.9674.34536.0572-0.72920.4184-0.80761.4964-0.16662.23170.3509-0.07980.85351.5689-0.43830.2831.5662-0.11871.2061-99.6358-4.33457.4893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -2:163)
2X-RAY DIFFRACTION2(chain A and resid 164:252)
3X-RAY DIFFRACTION3(chain A and resid 253:300)
4X-RAY DIFFRACTION4(chain A and resid 301:354)
5X-RAY DIFFRACTION5(chain A and resid 355:414)
6X-RAY DIFFRACTION6(chain A and resid 415:491)
7X-RAY DIFFRACTION7(chain A and resid 492:523)
8X-RAY DIFFRACTION8(chain A and resid 524:569)
9X-RAY DIFFRACTION9(chain B and resid 10:29)
10X-RAY DIFFRACTION10(chain B and resid 30:77)
11X-RAY DIFFRACTION11(chain B and resid 78:177)
12X-RAY DIFFRACTION12(chain B and resid 178:289)
13X-RAY DIFFRACTION13(chain B and resid 290:351)
14X-RAY DIFFRACTION14(chain B and resid 352:485)
15X-RAY DIFFRACTION15(chain B and resid 486:569)
16X-RAY DIFFRACTION16(chain B and resid 570:593)

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