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- PDB-4hlu: Structure of the EcfA-A' heterodimer bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4hlu
TitleStructure of the EcfA-A' heterodimer bound to ADP
Components
  • Energy-coupling factor transporter ATP-binding protein EcfA
  • Putative ABC transporter ATP-binding protein TM_0222
KeywordsHYDROLASE / Membrane transport / Vitamin uptake / Energy coupling factor transporter / ATPase / ATP-binding casette
Function / homology
Function and homology information


Translocases / riboflavin transport / riboflavin transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / 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 ...Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7003 Å
AuthorsWang, D.N. / Karpowich, N.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Assembly and mechanism of a group II ECF transporter.
Authors: Karpowich, N.K. / Wang, D.N.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Putative ABC transporter ATP-binding protein TM_0222
D: Energy-coupling factor transporter ATP-binding protein EcfA
B: Putative ABC transporter ATP-binding protein TM_0222
C: Energy-coupling factor transporter ATP-binding protein EcfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,50413
Polymers120,5004
Non-polymers2,0049
Water1,60389
1
A: Putative ABC transporter ATP-binding protein TM_0222
D: Energy-coupling factor transporter ATP-binding protein EcfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2236
Polymers60,2502
Non-polymers9724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-25 kcal/mol
Surface area23650 Å2
MethodPISA
2
B: Putative ABC transporter ATP-binding protein TM_0222
C: Energy-coupling factor transporter ATP-binding protein EcfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2827
Polymers60,2502
Non-polymers1,0325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-26 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.785, 67.785, 252.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:265 )
211chain 'B' and (resseq 1:265 )
112chain 'D' and (resseq 999:1003 or resseq 1008:1247 )
212chain 'C' and (resseq 999:1003 or resseq 1008:1247 )

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative ABC transporter ATP-binding protein TM_0222


Mass: 30390.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0222, TM_0222 / Plasmid: pACYC-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WY65, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Protein Energy-coupling factor transporter ATP-binding protein EcfA / ECF transporter A component EcfA


Mass: 29859.945 Da / Num. of mol.: 2 / Mutation: K2R, T4E, E53A, E55A, E125A, K126A, E127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: cbiO, ecfA, TM1663, TM_1663 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X1Z1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM sodium acetate, 30% MPD, 200mM sodium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→48.15 Å / Num. all: 36024 / Num. obs: 35999 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Biso Wilson estimate: 54.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 37.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YZ2

2yz2


Resolution: 2.7003→48.15 Å / SU ML: 0.38 / σ(F): 2.01 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1758 4.94 %Random
Rwork0.2133 ---
obs0.2155 35599 99.93 %-
all-36024 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.776 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5047 Å20 Å20 Å2
2--1.5047 Å2-0 Å2
3---3.4938 Å2
Refinement stepCycle: LAST / Resolution: 2.7003→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 128 89 8336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078408
X-RAY DIFFRACTIONf_angle_d1.13311353
X-RAY DIFFRACTIONf_dihedral_angle_d18.0423160
X-RAY DIFFRACTIONf_chiral_restr0.071268
X-RAY DIFFRACTIONf_plane_restr0.0041447
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2119X-RAY DIFFRACTIONPOSITIONAL
12B2119X-RAY DIFFRACTIONPOSITIONAL0.071
21D1923X-RAY DIFFRACTIONPOSITIONAL
22C1923X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-2.77330.38721380.32272589X-RAY DIFFRACTION100
2.7733-2.85490.34691280.2992619X-RAY DIFFRACTION100
2.8549-2.9470.3391440.28192664X-RAY DIFFRACTION100
2.947-3.05230.31641220.282545X-RAY DIFFRACTION100
3.0523-3.17450.32451360.27372607X-RAY DIFFRACTION100
3.1745-3.3190.28961380.25612602X-RAY DIFFRACTION100
3.319-3.49390.28071360.23622601X-RAY DIFFRACTION100
3.4939-3.71270.24961300.20762619X-RAY DIFFRACTION100
3.7127-3.99920.21081380.19452631X-RAY DIFFRACTION100
3.9992-4.40150.22581440.17642556X-RAY DIFFRACTION100
4.4015-5.03780.21731290.17622609X-RAY DIFFRACTION100
5.0378-6.34480.24451420.21882600X-RAY DIFFRACTION100
6.3448-48.15720.24461330.17152599X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 61.4401 Å / Origin y: 43.9638 Å / Origin z: 0.9563 Å
111213212223313233
T-0.2374 Å2-0.1056 Å2-0.0908 Å2-0.1363 Å2-0.091 Å2--0.0302 Å2
L0.1535 °2-0.0028 °20.103 °2-0.1589 °20.0309 °2--0.1168 °2
S-0.1362 Å °-0.0916 Å °-0.0016 Å °-0.2737 Å °0.2275 Å °-0.2333 Å °-0.1662 Å °0.0941 Å °0.2711 Å °
Refinement TLS groupSelection details: all

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