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- PDB-5dgx: 1.73 Angstrom resolution crystal structure of the ABC-ATPase doma... -

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Basic information

Entry
Database: PDB / ID: 5dgx
Title1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsTRANSPORT PROTEIN / Lipid A transport protein / ABC transporter / ATP-binding and membrane protein / Francisella tularensis subsp. tularensis SCHU S4 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / 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 ...Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.73 Angstrom resolution crystal structure of the ABC-ATPase domain (residues 357-609) of lipid A transport protein (msbA) from Francisella tularensis subsp. tularensis SCHU S4 in complex with ADP
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid A export ATP-binding/permease protein MsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2702
Polymers27,8431
Non-polymers4271
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.597, 70.886, 46.647
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipid A export ATP-binding/permease protein MsbA


Mass: 27843.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain FSC 198) (bacteria)
Strain: FSC 198 / Gene: msbA, FTF0109 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-magic
References: UniProt: Q14JW6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein: 8.2 mg/ml in 10 mM Tris-HCl pH 8.3 0.5 mM TCEP 10 mM ADP 10 mM MgCl2 crystallization: The Classics II F11 (71): 0.2 M NaCl 0.1 M Bis-Tris pH 6.5 25% (w/v) PEG 3350 cryo: crystallization condition

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2015
RadiationMonochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 23573 / % possible obs: 90.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.3
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
Cootmodel building
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fgk

2fgk


Resolution: 1.73→21.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.98 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23282 1199 5.1 %RANDOM
Rwork0.19437 ---
obs0.19635 22233 89.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.581 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20 Å2-1.28 Å2
2---0.11 Å20 Å2
3---3.28 Å2
Refinement stepCycle: 1 / Resolution: 1.73→21.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 27 193 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191892
X-RAY DIFFRACTIONr_bond_other_d0.0010.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9772566
X-RAY DIFFRACTIONr_angle_other_deg0.834175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.695244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66225.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24315339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5831510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.732→1.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 90 -
Rwork0.265 1726 -
obs--95.48 %
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)
10.9530.005-0.60360.91810.09241.35520.04030.07080.05390.1275-0.0295-0.0752-0.10340.0301-0.01080.09510.00410.02310.05760.01730.027817.307941.012341.4769
25.4966-2.9428-0.41793.5509-0.63493.20760.18080.34260.217-0.3943-0.0318-0.220.04730.1098-0.1490.1243-0.0180.04270.23860.00470.02942.901237.676420.8002
33.8737-0.88391.92041.1573-0.69241.53610.0780.2548-0.2986-0.08150.03550.08390.2060.0062-0.11350.1106-0.01560.03010.154-0.00850.03831.465535.217727.0332
40.94010.5748-0.67532.426-0.90211.23220.0042-0.0128-0.1010.2374-0.05170.03730.1008-0.01940.04750.12270.00320.0420.0180.00770.0349.817425.146649.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A358 - 452
2X-RAY DIFFRACTION2A453 - 487
3X-RAY DIFFRACTION3A488 - 557
4X-RAY DIFFRACTION4A558 - 609

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