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- PDB-4y6c: Q17M crystal structure of Podosopora anserina putative kinesin li... -

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Basic information

Entry
Database: PDB / ID: 4y6c
TitleQ17M crystal structure of Podosopora anserina putative kinesin light chain nearly identical TPR-like repeats
ComponentsANSERINA PUTATIVE KINESIN LIGHT chain
KeywordsUNKNOWN FUNCTION / Tetratricopeptide repeat / 42PR / TPR
Function / homology
Function and homology information


NB-ARC / NB-ARC domain / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.772 Å
AuthorsMarold, J.D. / Kavran, J.M. / Bowman, G.D. / Barrick, D.
CitationJournal: Structure / Year: 2015
Title: A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins.
Authors: Marold, J.D. / Kavran, J.M. / Bowman, G.D. / Barrick, D.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANSERINA PUTATIVE KINESIN LIGHT chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2163
Polymers26,0241
Non-polymers1922
Water3,045169
1
A: ANSERINA PUTATIVE KINESIN LIGHT chain
hetero molecules

A: ANSERINA PUTATIVE KINESIN LIGHT chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4316
Polymers52,0472
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4850 Å2
ΔGint-48 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.103, 91.242, 30.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsdetermined by Analytical Ultracentrifugation Sedimentation Velocity

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Components

#1: Protein ANSERINA PUTATIVE KINESIN LIGHT chain / Q17M


Mass: 26023.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Strain: S mat+ / Gene: CDP31375.1 / Plasmid: pET15b / Cell line (production host): ROSETTA 2 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: A0A090CRQ5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 295.16 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, 35% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.772→39.76 Å / Num. all: 23011 / Num. obs: 23013 / % possible obs: 99.97 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.175 / Rsym value: 0.172 / Net I/σ(I): 17.7
Reflection shellResolution: 1.773→1.836 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 11.4 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Coot0.6.2model building
SHELXDEphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.772→39.76 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1161 5.05 %Random selection
Rwork0.173 ---
obs0.175 23011 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.772→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 10 169 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061761
X-RAY DIFFRACTIONf_angle_d0.9222386
X-RAY DIFFRACTIONf_dihedral_angle_d17.576698
X-RAY DIFFRACTIONf_chiral_restr0.037267
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7724-1.85310.24741440.18192664X-RAY DIFFRACTION99
1.8531-1.95080.23081510.17042651X-RAY DIFFRACTION100
1.9508-2.0730.21831410.17442726X-RAY DIFFRACTION100
2.073-2.2330.21281230.16522699X-RAY DIFFRACTION100
2.233-2.45770.21391530.16512703X-RAY DIFFRACTION100
2.4577-2.81330.21211360.17852749X-RAY DIFFRACTION100
2.8133-3.54410.21771550.17912747X-RAY DIFFRACTION100
3.5441-39.7720.19861580.17062911X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.48 Å / Origin y: -40.3489 Å / Origin z: -0.4465 Å
111213212223313233
T0.0711 Å20.0063 Å20.0076 Å2-0.0891 Å2-0.0081 Å2--0.0546 Å2
L0.4883 °2-0.0667 °20.0381 °2-1.225 °2-0.1217 °2--0.3766 °2
S0.0242 Å °0.0121 Å °0.0235 Å °0.0206 Å °-0.0138 Å °-0.0609 Å °-0.0194 Å °-0.0165 Å °-0.0116 Å °
Refinement TLS groupSelection details: all

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