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- PDB-3zik: Structure of the Wpl1 protein -

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Basic information

Entry
Database: PDB / ID: 3zik
TitleStructure of the Wpl1 protein
ComponentsWPL1
KeywordsCELL CYCLE / COHESIN / CHROMOSOME SEGREGATION
Function / homologyRad61, Wapl domain / Rad61, Wapl domain / Rad61, Wapl domain superfamily / Wap1 domain / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / AAR187Cp
Function and homology information
Biological speciesEREMOTHECIUM GOSSYPII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.14 Å
AuthorsChatterjee, A. / Zakian, S. / Hu, X.-W. / Singleton, M.R.
CitationJournal: Embo J. / Year: 2013
Title: Structural Insights Into Regulation of Cohesion Establishment by Wpl1
Authors: Chatterjee, A. / Zakian, S. / Hu, X.-W. / Singleton, M.R.
History
DepositionJan 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WPL1
B: WPL1


Theoretical massNumber of molelcules
Total (without water)85,7462
Polymers85,7462
Non-polymers00
Water2,468137
1
A: WPL1


Theoretical massNumber of molelcules
Total (without water)42,8731
Polymers42,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WPL1


Theoretical massNumber of molelcules
Total (without water)42,8731
Polymers42,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 62.870, 63.270
Angle α, β, γ (deg.)99.97, 110.91, 99.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WPL1 / AAR187CP


Mass: 42873.230 Da / Num. of mol.: 2 / Fragment: RESIDUES 184-561 / Source method: isolated from a natural source / Source: (natural) EREMOTHECIUM GOSSYPII (fungus) / References: UniProt: Q75E93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.49 Å3/Da / Density % sol: 50.59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.972
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 44611 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.822 / % possible all: 94.2

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.14→36.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.718 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24033 2251 5.1 %RANDOM
Rwork0.18258 ---
obs0.18552 41927 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0.12 Å20.28 Å2
2--0.11 Å20.14 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.14→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 0 137 5916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9747979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33124.28257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.749151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9811535
X-RAY DIFFRACTIONr_chiral_restr0.1280.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214300
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 164 -
Rwork0.265 3078 -
obs--96.49 %

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