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- PDB-5f9q: Crystal structure of the extracellular domain of noncanonic ABC-t... -

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Basic information

Entry
Database: PDB / ID: 5f9q
TitleCrystal structure of the extracellular domain of noncanonic ABC-type transporter YknZ from Gram-positive bacteria
ComponentsMacrolide export ATP-binding/permease protein YknZ
KeywordsMEMBRANE PROTEIN / Bacillus amyloliquefaciens / SDP transporter YknWXYZ / respective permease YknZ
Function / homology:
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.044 Å
AuthorsXu, Y. / Guo, J. / Jiang, R. / Jin, X. / Fan, S. / Quan, C.S. / Ha, N.C.
Funding support China, 5items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31200556 China
the National Natural Science Foundation of China21402024 China
the National Natural Science Foundation of China21272031 China
China Postdoctoral Science Foundation2013M540229 China
the Fundamental Research Funds for the Central UniversitiesDC201502020203 China
CitationJournal: Plos One / Year: 2016
Title: The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens.
Authors: Xu, Y. / Guo, J. / Wang, L. / Jiang, R. / Jin, X. / Liu, J. / Fan, S. / Quan, C.S. / Ha, N.C.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Macrolide export ATP-binding/permease protein YknZ


Theoretical massNumber of molelcules
Total (without water)22,0831
Polymers22,0831
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-12 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.169, 46.147, 87.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22082.582 Da / Num. of mol.: 1 / Fragment: Extracellural domain (UNP RESIDUES 58-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: ABH13_1432 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3VAX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 4.6
Details: 22.5% (w/v) polyethylene glycol 4000, 0.125 M ammonium acetate, 0.1 M sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→41 Å / Num. obs: 11741 / % possible obs: 95.8 % / Redundancy: 4.7 % / Net I/σ(I): 12.6
Reflection shellResolution: 2→10 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 12.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data processing
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.044→40.823 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2473 1166 9.93 %
Rwork0.1944 --
obs0.1996 11741 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.044→40.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 97 1530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011452
X-RAY DIFFRACTIONf_angle_d1.1571954
X-RAY DIFFRACTIONf_dihedral_angle_d16.574539
X-RAY DIFFRACTIONf_chiral_restr0.043221
X-RAY DIFFRACTIONf_plane_restr0.006254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0441-2.13710.3491480.29451269X-RAY DIFFRACTION99
2.1371-2.24980.30561340.25941284X-RAY DIFFRACTION98
2.2498-2.39070.29591390.23411276X-RAY DIFFRACTION97
2.3907-2.57530.27721410.21731328X-RAY DIFFRACTION100
2.5753-2.83440.29741490.21731312X-RAY DIFFRACTION100
2.8344-3.24440.26561490.19351330X-RAY DIFFRACTION100
3.2444-4.0870.22931490.16031350X-RAY DIFFRACTION100
4.087-40.83060.18441570.16381426X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.423 Å / Origin y: 18.5962 Å / Origin z: 20.0147 Å
111213212223313233
T0.1755 Å2-0.0097 Å20.0051 Å2-0.1581 Å2-0.0043 Å2--0.1732 Å2
L1.1044 °2-0.1371 °20.6265 °2-0.805 °2-0.2936 °2--1.2144 °2
S-0.0253 Å °-0.0018 Å °-0.0641 Å °0.0308 Å °0.0502 Å °0.0388 Å °0.0254 Å °-0.0684 Å °-0.0085 Å °
Refinement TLS groupSelection details: all

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