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- PDB-1kcf: Crystal Structure of the Yeast Mitochondrial Holliday Junction Re... -

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Basic information

Entry
Database: PDB / ID: 1kcf
TitleCrystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2
ComponentsHYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I
KeywordsHYDROLASE / beta-alpha-beta motif / RuvC resolvase family
Function / homology
Function and homology information


crossed form four-way junction DNA binding / crossover junction endodeoxyribonuclease / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / : / four-way junction DNA binding / DNA endonuclease activity / mitochondrion ...crossed form four-way junction DNA binding / crossover junction endodeoxyribonuclease / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / : / four-way junction DNA binding / DNA endonuclease activity / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Mitochondrial resolvase Ydc2, catalytic / Mrs1/Cce1 / Mitochondrial resolvase Ydc2 / RNA splicing MRS1 / SAP domain superfamily / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Mitochondrial resolvase Ydc2, catalytic / Mrs1/Cce1 / Mitochondrial resolvase Ydc2 / RNA splicing MRS1 / SAP domain superfamily / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cruciform cutting endonuclease 1, mitochondrial
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single Wavelength Anomalous Dispersion / Resolution: 2.3 Å
AuthorsCeschini, S. / Keeley, A. / McAlister, M.S.B. / Oram, M. / Phelan, J. / Pearl, L.H. / Tsaneva, I.R. / Barrett, T.E.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.
Authors: Ceschini, S. / Keeley, A. / McAlister, M.S. / Oram, M. / Phelan, J. / Pearl, L.H. / Tsaneva, I.R. / Barrett, T.E.
History
DepositionNov 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I
B: HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6884
Polymers60,4962
Non-polymers1922
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-38 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.000, 133.940, 73.250
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 HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I


Mass: 30247.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC25G10.02 / Plasmid: pET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q10423, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.9257.86
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2871microbatch4.6Ammonium Sulphate, Sodium acetate, pH 4.6, microbatch, temperature 287K
2872microbatch8.5Dihydrogen Phosphate, Tris-Hcl, pH 8.5, microbatch, temperature 287K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 Mammonium sulfate11or dihydrogen phosphate
20.1 Msodium acetate11pH4.6
30.1 MTris-HCl11pH8.5
40.5 Mlithium sulfate monohydrate11
515 %(w/v)PEG800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2001 / Details: Mirrors
RadiationMonochromator: Sagitally focused Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→29.34 Å / Num. all: 35212 / Num. obs: 31239 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.034 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4787 / Rsym value: 0.17 / % possible all: 90.5
Reflection
*PLUS
Redundancy: 3.4 % / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
Rmerge(I) obs: 0.219

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Processing

Software
NameVersionClassification
SOLVEphasing
RESOLVEmodel building
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: Single Wavelength Anomalous Dispersion
Resolution: 2.3→29.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1517194.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used bulk solvent correction, simulated annealing, energy minimization, overall and indvidual B-factor refinement. A maximum likelihood refinent target was also used.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1518 5 %RANDOM
Rwork0.238 ---
all0.242 31239 --
obs0.242 31239 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.7635 Å2 / ksol: 0.366887 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.7 Å20 Å20 Å2
2---7.53 Å20 Å2
3----6.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 10 220 3968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 236 4.9 %
Rwork0.268 4551 -
obs-4787 90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.268

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