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- PDB-3ftj: Crystal structure of the periplasmic region of MacB from Actinoba... -

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Basic information

Entry
Database: PDB / ID: 3ftj
TitleCrystal structure of the periplasmic region of MacB from Actinobacillus actinomycetemcomitans
ComponentsMacrolide export ATP-binding/permease protein macB
KeywordsHYDROLASE / macrolide-specific pump / ABC-type transporter / heat stable exotoxin II / membrane protein / periplasmic region / Antibiotic resistance / ATP-binding / Cell inner membrane / Cell membrane / Membrane / Nucleotide-binding / Transmembrane / Transport
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Macrolide export ATP-binding/permease protein macB family profile. / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...Macrolide export ATP-binding/permease protein macB family profile. / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesActinobacillus actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.999 Å
AuthorsXu, Y. / Ha, N.C.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of the periplasmic region of MacB, a noncanonic ABC transporter
Authors: Xu, Y. / Sim, S.-H. / Nam, K.H. / Jin, X.L. / Kim, H.-M. / Hwang, K.Y. / Lee, K. / Ha, N.-C.
History
DepositionJan 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrolide export ATP-binding/permease protein macB


Theoretical massNumber of molelcules
Total (without water)24,7271
Polymers24,7271
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.444, 108.444, 92.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE FULL-LENGTH MACB WAS CONFIRMED AS A HOMODIMER. HOWEVER, ONLY THE PERIPLASMIC REGION BEHAVED AS A MONOMER ON A SIZE EXCLUSION CHROMATOGRAPHY, PERFORMED BY THE DEPOSITORS RESEARCH GROUP. THUS THEY SPECULATE THAT THE DIMERIC FORMATION OF FULL-LENGTH MACB IS RESPONSIBLE FOR THE CYTOPLASMIC NBD OR THE TRANSMEMBRANE SEGMENT.

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Components

#1: Protein Macrolide export ATP-binding/permease protein macB / MacB


Mass: 24726.875 Da / Num. of mol.: 1 / Fragment: periplasmic region, UNP residues 293-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus actinomycetemcomitans (bacteria)
Gene: macB, MACB_ACTAC / Plasmid: pPROEX-HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q2EHL8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1% PEG 400, 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 4A20.97943, 0.97963, 0.97175
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMay 5, 2008double mirror
ADSC QUANTUM 3152CCDJun 15, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1sillicon crystal, double mirrorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979431
30.979631
40.971751
ReflectionResolution: 2→50 Å / Num. all: 14360 / Num. obs: 13829 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1075 / Rsym value: 0.321 / % possible all: 76

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.999→33.158 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / Data cutoff high absF: 47369.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.12 / σ(I): 0 / Phase error: 24.77 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 694 5.02 %RANDOM
Rwork0.1995 ---
obs0.202 13828 50.13 %-
all-14360 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.295 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 78.29 Å2 / Biso mean: 31.375 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.817 Å2-0 Å2-0 Å2
2--1.817 Å20 Å2
3----3.634 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.999→33.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 0 139 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061668
X-RAY DIFFRACTIONf_angle_d0.9582248
X-RAY DIFFRACTIONf_dihedral_angle_d17.604619
X-RAY DIFFRACTIONf_chiral_restr0.066267
X-RAY DIFFRACTIONf_plane_restr0.003290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.15360.32741250.2582265X-RAY DIFFRACTION44
2.1536-2.37030.26341400.21452654X-RAY DIFFRACTION51
2.3703-2.71310.2481470.20612681X-RAY DIFFRACTION51
2.7131-3.41770.24861510.19252705X-RAY DIFFRACTION52
3.4177-33.16270.22051310.1832829X-RAY DIFFRACTION53
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ater_rep.paramwater.top

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