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- PDB-7f0k: Crystal structure of Kmp11 -

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Basic information

Entry
Database: PDB / ID: 7f0k
TitleCrystal structure of Kmp11
ComponentsKinetoplastid membrane protein KMP-11
KeywordsLIPID BINDING PROTEIN / Kmp11 / kinetoplastid / membrane BINDING PROTEIN
Function / homologyKinetoplastid membrane protein 11 / Kinetoplastid membrane protein 11 / defense response / microtubule / positive regulation of cell population proliferation / cytoplasm / Kinetoplastid membrane protein KMP-11
Function and homology information
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsMo, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071476 China
CitationJournal: To be published
Title: Structural insight into dynamic characteristic of the polymerized forms of kinetoplastid membrane protein-11
Authors: Mo, X.
History
DepositionJun 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinetoplastid membrane protein KMP-11
B: Kinetoplastid membrane protein KMP-11


Theoretical massNumber of molelcules
Total (without water)22,6662
Polymers22,6662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, ~Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-31 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.899, 38.544, 142.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYS(chain 'A' and resid 4 through 80)AA4 - 214 - 21
12GLUGLUPROPRO(chain 'A' and resid 4 through 80)AA24 - 4224 - 42
13LYSLYSGLUGLU(chain 'A' and resid 4 through 80)AA45 - 5245 - 52
14ILEILELYSLYS(chain 'A' and resid 4 through 80)AA55 - 6455 - 64
15ARGARGGLUGLU(chain 'A' and resid 4 through 80)AA67 - 7967 - 79
26THRTHRLYSLYSchain 'B'BB4 - 214 - 21
27GLUGLUPROPROchain 'B'BB24 - 4224 - 42
28LYSLYSGLUGLUchain 'B'BB45 - 5245 - 52
29ILEILELYSLYSchain 'B'BB55 - 6455 - 64
210ARGARGGLUGLUchain 'B'BB67 - 7967 - 79

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Components

#1: Protein Kinetoplastid membrane protein KMP-11


Mass: 11333.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972) (eukaryote)
Strain: MHOM/CI/86/DAL972
Gene: TbgDal_IX8640, TbgDal_IX8650, TbgDal_IX8660, TbgDal_IX8670
Production host: Escherichia coli (E. coli) / References: UniProt: C9ZZD9
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 2583 / % possible obs: 99.16 % / Redundancy: 3.1 % / Biso Wilson estimate: 47.8 Å2 / CC1/2: 0.8 / Net I/σ(I): 9
Reflection shellResolution: 3.5→3.625 Å / Num. unique obs: 236 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→31.32 Å / SU ML: 0.4629 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2984 128 4.96 %
Rwork0.2574 2453 -
obs0.2594 2581 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 3.5→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 0 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151424
X-RAY DIFFRACTIONf_angle_d0.33411888
X-RAY DIFFRACTIONf_chiral_restr0.0273181
X-RAY DIFFRACTIONf_plane_restr0.0037249
X-RAY DIFFRACTIONf_dihedral_angle_d3.1653171
LS refinement shellHighest resolution: 3.5 Å
RfactorNum. reflection% reflection
Rfree0.2984 128 -
Rwork0.2574 2453 -
obs--96.52 %

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