- PDB-1o12: Crystal structure of N-acetylglucosamine-6-phosphate deacetylase ... -
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Basic information
Entry
Database: PDB / ID: 1o12
Title
Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution
Components
N-acetylglucosamine-6-phosphate deacetylase
Keywords
HYDROLASE / STRUCTURAL GENOMICS / TM0814 / N-acetylglucosamine-6-phosphate deacetylase / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information
N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / carbohydrate metabolic process / metal ion binding Similarity search - Function
BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.
Resolution: 2.5→42.533 Å / Num. obs: 30706 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 58.5 Å2 / Rsym value: 0.069 / Net I/σ(I): 19
Reflection shell
Resolution: 2.5→2.57 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 5 / Rsym value: 0.408 / % possible all: 100
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Processing
Software
Name
Version
Classification
MOSFLM
datareduction
CCP4
datareduction
SCALEPACK
datascaling
SnB
phasing
MLPHARE
phasing
CCP4
modelbuilding
SOLVE
phasing
CNS
1
refinement
CCP4
datascaling
CCP4
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.5→42.53 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER Details: EXTRA DENSITY NEAR THE N-TERMINUS. N-TERMINUS FROM SYMMETRY RELATED MOLECULES ARE CLOSE AND THE EXTRA DENSITY COULD NOT EASILY BE INTERPRETED. THERE ARE TWO MONOMERS IN THE ASYMMETRIC UNIT ...Details: EXTRA DENSITY NEAR THE N-TERMINUS. N-TERMINUS FROM SYMMETRY RELATED MOLECULES ARE CLOSE AND THE EXTRA DENSITY COULD NOT EASILY BE INTERPRETED. THERE ARE TWO MONOMERS IN THE ASYMMETRIC UNIT WITH 363 RESIDUES PER MONOMER. THE C-TERMINAL RESIDUES (ARG 364) IN BOTH MONOMERS ARE DISORDERED. REFINEMENTS STARTED WITH NCS AND THE NCS RELEASED DURING THE FINAL STAGES. ONE FE ATOM PER MONOMER. THE FE ATOM IN THE TM0814 WAS ASSIGNED BASED ON THE DENSITY, COORDINATION, AND THE PRESENCE OF A FE ATOM AT THIS POSITION IN THE CYTOSINE DEAMINASE STRUCTURE. THE LOWER NUMBER OF RESIDUES IN THE CORE REGION SEEMS TO BE RELATED TO THE TYPE OF FOLD.
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