- PDB-1kcf: Crystal Structure of the Yeast Mitochondrial Holliday Junction Re... -
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Basic information
Entry
Database: PDB / ID: 1kcf
Title
Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2
Components
HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I
Keywords
HYDROLASE / beta-alpha-beta motif / RuvC resolvase family
Function / homology
Function and homology information
mitochondrial chromosome / crossover junction endodeoxyribonuclease / crossed form four-way junction DNA binding / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / four-way junction DNA binding / DNA endonuclease activity ...mitochondrial chromosome / crossover junction endodeoxyribonuclease / crossed form four-way junction DNA binding / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / 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
Resolution: 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
Name
Version
Classification
SOLVE
phasing
RESOLVE
modelbuilding
CNS
1
refinement
DENZO
datareduction
CCP4
(SCALA)
datascaling
RESOLVE
phasing
Refinement
Method 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.
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