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

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Basic information

Entry
Database: PDB / ID: 3zil
TitleStructure of the Wpl1 protein
Components
  • AAL182WP
  • AAR187CP
KeywordsCELL CYCLE / COHESIN / CHROMOSOME SEGREGATION
Function / homology
Function and homology information


topological DNA co-entrapment activity / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / condensed chromosome, centromeric region => GO:0000779 / cohesin loader activity / synaptonemal complex assembly / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / reciprocal meiotic recombination ...topological DNA co-entrapment activity / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / condensed chromosome, centromeric region => GO:0000779 / cohesin loader activity / synaptonemal complex assembly / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / reciprocal meiotic recombination / cell division / protein kinase binding / ATP binding / identical protein binding
Similarity search - Function
Rad61, Wapl domain / Rad61, Wapl domain / Rad61, Wapl domain superfamily / Wap1 domain / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain ...Rad61, Wapl domain / Rad61, Wapl domain / Rad61, Wapl domain superfamily / Wap1 domain / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Leucine-rich Repeat Variant / Alpha Horseshoe / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
AAR187Cp / Structural maintenance of chromosomes protein
Similarity search - Component
Biological speciesEREMOTHECIUM GOSSYPII (fungus)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.012 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: AAR187CP
B: AAL182WP


Theoretical massNumber of molelcules
Total (without water)46,1422
Polymers46,1422
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7.9 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.402, 35.207, 117.381
Angle α, β, γ (deg.)90.00, 101.89, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein AAR187CP / WPL1


Mass: 42873.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 184-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EREMOTHECIUM GOSSYPII (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q75E93
#2: Protein/peptide AAL182WP / SMC3


Mass: 3268.658 Da / Num. of mol.: 1 / Fragment: RESIDUES 136-163 / Source method: obtained synthetically / Source: (synth.) EREMOTHECIUM GOSSYPII (fungus) / References: UniProt: Q75FB3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.13 Å3/Da / Density % sol: 42.37 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 26061 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3

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Processing

SoftwareName: REFMAC / Version: 5.6 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.012→29.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.581 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24567 1322 5.1 %RANDOM
Rwork0.19964 ---
obs0.20204 24737 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.05 Å2
2--0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.012→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 0 61 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9744107
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76924.403134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14415546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571518
X-RAY DIFFRACTIONr_chiral_restr0.1340.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212224
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: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 73 -
Rwork0.34 1573 -
obs--89.6 %

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