- PDB-3kip: Crystal structure of type-II 3-dehydroquinase from C. albicans -
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Basic information
Entry
Database: PDB / ID: 3kip
Title
Crystal structure of type-II 3-dehydroquinase from C. albicans
Components
3-dehydroquinase, type II
Keywords
LYASE
Function / homology
Function and homology information
quinate metabolic process / 3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. Authors: Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel / Abstract: The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing ...The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.
#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (6)
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Assembly
Deposited unit
A: 3-dehydroquinase, type II B: 3-dehydroquinase, type II C: 3-dehydroquinase, type II D: 3-dehydroquinase, type II E: 3-dehydroquinase, type II F: 3-dehydroquinase, type II G: 3-dehydroquinase, type II H: 3-dehydroquinase, type II I: 3-dehydroquinase, type II J: 3-dehydroquinase, type II K: 3-dehydroquinase, type II L: 3-dehydroquinase, type II M: 3-dehydroquinase, type II N: 3-dehydroquinase, type II O: 3-dehydroquinase, type II P: 3-dehydroquinase, type II Q: 3-dehydroquinase, type II R: 3-dehydroquinase, type II S: 3-dehydroquinase, type II T: 3-dehydroquinase, type II U: 3-dehydroquinase, type II V: 3-dehydroquinase, type II W: 3-dehydroquinase, type II X: 3-dehydroquinase, type II hetero molecules
A: 3-dehydroquinase, type II B: 3-dehydroquinase, type II C: 3-dehydroquinase, type II D: 3-dehydroquinase, type II E: 3-dehydroquinase, type II F: 3-dehydroquinase, type II G: 3-dehydroquinase, type II H: 3-dehydroquinase, type II I: 3-dehydroquinase, type II J: 3-dehydroquinase, type II K: 3-dehydroquinase, type II L: 3-dehydroquinase, type II hetero molecules
M: 3-dehydroquinase, type II N: 3-dehydroquinase, type II O: 3-dehydroquinase, type II P: 3-dehydroquinase, type II Q: 3-dehydroquinase, type II R: 3-dehydroquinase, type II S: 3-dehydroquinase, type II T: 3-dehydroquinase, type II U: 3-dehydroquinase, type II V: 3-dehydroquinase, type II W: 3-dehydroquinase, type II X: 3-dehydroquinase, type II hetero molecules
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.95→70.68 Å / Num. all: 101344 / Num. obs: 101228 / % possible obs: 99.89 % / Redundancy: 6.4 % / Biso Wilson estimate: 77.8 Å2 / Rsym value: 0.136 / Net I/σ(I): 4.3
Reflection shell
Resolution: 2.95→3.11 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 14646 / Rsym value: 0.539 / % possible all: 100
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
MOSFLM
datareduction
SCALA
3.3.9
datascaling
AMoRE
phasing
REFMAC
refinement
PDB_EXTRACT
3.005
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: a 3D EM reconstruction at 15 A resolution Resolution: 2.95→70.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.963 / SU B: 34.706 / SU ML: 0.299 / SU R Cruickshank DPI: 0.339 / SU Rfree: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
5090
5 %
RANDOM
Rwork
0.203
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obs
0.205
101228
99.89 %
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all
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101344
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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