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- PDB-5x7k: Crystal structure of the nucleotide-binding domain (NBD) of LipB,... -

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Basic information

Entry
Database: PDB / ID: 5x7k
TitleCrystal structure of the nucleotide-binding domain (NBD) of LipB, a ABC transporter subunit of a type I secretion system
ComponentsLipase B
KeywordsTRANSPORT PROTEIN / ABC transporter / walker A / walker B / NBD / nucleotide binding domain / type I secretion system / T1SS / protein secretion / translocation system
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
ATPase, type I secretion system, PrtD-like / : / 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 ...ATPase, type I secretion system, PrtD-like / : / 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
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsOkano, H. / Angkawidjaja, C. / Takano, K.
CitationJournal: Biochemistry / Year: 2017
Title: Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain
Authors: Murata, D. / Okano, H. / Angkawidjaja, C. / Akutsu, M. / Tanaka, S.I. / Kitahara, K. / Yoshizawa, T. / Matsumura, H. / Kado, Y. / Mizohata, E. / Inoue, T. / Sano, S. / Koga, Y. / Kanaya, S. / Takano, K.
History
DepositionFeb 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase B
B: Lipase B


Theoretical massNumber of molelcules
Total (without water)56,9632
Polymers56,9632
Non-polymers00
Water1,06359
1
A: Lipase B


Theoretical massNumber of molelcules
Total (without water)28,4811
Polymers28,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase B


Theoretical massNumber of molelcules
Total (without water)28,4811
Polymers28,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.302, 61.298, 88.313
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase B


Mass: 28481.324 Da / Num. of mol.: 2 / Fragment: UNP residues 321-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: lipB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q54456
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.4M K2HPO4, 0.6M NaH2PO4, 0.1M imidazole pH 8.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 21754 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.081 / Χ2: 1.061 / Net I/av σ(I): 18.05 / Net I/σ(I): 18.05
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 996 / Χ2: 0.509 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→35.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.765 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26133 1116 5.1 %RANDOM
Rwork0.20447 ---
obs0.20752 20626 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.03 Å2
2---0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.65→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 59 3523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193512
X-RAY DIFFRACTIONr_bond_other_d00.023492
X-RAY DIFFRACTIONr_angle_refined_deg0.7131.9834774
X-RAY DIFFRACTIONr_angle_other_deg0.52638001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3755461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.94325.352142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.5515576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4391518
X-RAY DIFFRACTIONr_chiral_restr0.0490.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02748
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_it6.4625.2911858
X-RAY DIFFRACTIONr_mcbond_other6.4445.2911858
X-RAY DIFFRACTIONr_mcangle_it8.9987.9322314
X-RAY DIFFRACTIONr_mcangle_other9.0027.9342315
X-RAY DIFFRACTIONr_scbond_it7.8026.1091654
X-RAY DIFFRACTIONr_scbond_other7.8016.111655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.68.8162461
X-RAY DIFFRACTIONr_long_range_B_refined14.64665.353793
X-RAY DIFFRACTIONr_long_range_B_other14.64565.3663794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.648→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 57 -
Rwork0.345 1350 -
obs--86.96 %

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