10 20 30 40 50 60 70 80 1YUO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 14-FEB-05 1YUO
TITLE OPTIMISATION OF THE SURFACE ELECTROSTATICS AS A STRATEGY TITLE 2 FOR COLD ADAPTATION OF URACIL-DNA N-GLYCOSYLASE (UNG)FROM TITLE 3 ATLANTIC COD (GADUS MORHUA)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: UDG; COMPND 6 EC: 3.2.2.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UNG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NR8052; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRC99A
KEYWDS UNG, COLD ADAPTATION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.MOE,I.LEIROS,E.K.RIISE,M.OLUFSEN,O.LANES,A.O.SMALAS, AUTHOR 2 N.P.WILLASSEN
REVDAT 2 24-FEB-09 1YUO 1 VERSN REVDAT 1 01-MAR-05 1YUO 0
JRNL AUTH E.MOE,I.LEIROS,E.K.RIISE,M.OLUFSEN,O.LANES, JRNL AUTH 2 A.O.SMALAS,N.P.WILLASSEN JRNL TITL OPTIMISATION OF THE SURFACE ELECTROSTATICS AS A JRNL TITL 2 STRATEGY FOR COLD ADAPTATION OF URACIL-DNA JRNL TITL 3 N-GLYCOSYLASE (UNG) FROM ATLANTIC COD (GADUS JRNL TITL 4 MORHUA) JRNL REF J.MOL.BIOL. V. 343 1221 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15491608 JRNL DOI 10.1016/J.JMB.2004.09.004
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 14201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1443 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.66200 REMARK 3 B22 (A**2) : 6.11700 REMARK 3 B33 (A**2) : -11.77900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.23 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1YUO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB031937.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16602 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : 0.13200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY: 1AKZ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, SODIUM ACETATE, REMARK 280 PEG 8000, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 23.75550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.03550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.38550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.03550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.75550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.38550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 144 -81.77 -109.37 REMARK 500 GLN A 152 -68.04 -91.80 REMARK 500 HIS A 154 30.96 -153.10 REMARK 500 HIS A 212 24.42 44.98 REMARK 500 PRO A 269 -6.46 -59.32 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1YUO A 82 304 UNP P13051 UNG_HUMAN 91 313
SEQADV 1YUO MET A 82 UNP P13051 PRO 91 ENGINEERED SEQADV 1YUO GLU A 83 UNP P13051 VAL 92 ENGINEERED SEQADV 1YUO PHE A 84 UNP P13051 GLY 93 ENGINEERED SEQADV 1YUO VAL A 171 UNP P13051 GLU 180 ENGINEERED
SEQRES 1 A 223 MET GLU PHE PHE GLY GLU SER TRP LYS LYS HIS LEU SER SEQRES 2 A 223 GLY GLU PHE GLY LYS PRO TYR PHE ILE LYS LEU MET GLY SEQRES 3 A 223 PHE VAL ALA GLU GLU ARG LYS HIS TYR THR VAL TYR PRO SEQRES 4 A 223 PRO PRO HIS GLN VAL PHE THR TRP THR GLN MET CYS ASP SEQRES 5 A 223 ILE LYS ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP PRO SEQRES 6 A 223 TYR HIS GLY PRO ASN GLN ALA HIS GLY LEU CYS PHE SER SEQRES 7 A 223 VAL GLN ARG PRO VAL PRO PRO PRO PRO SER LEU VAL ASN SEQRES 8 A 223 ILE TYR LYS GLU LEU SER THR ASP ILE GLU ASP PHE VAL SEQRES 9 A 223 HIS PRO GLY HIS GLY ASP LEU SER GLY TRP ALA LYS GLN SEQRES 10 A 223 GLY VAL LEU LEU LEU ASN ALA VAL LEU THR VAL ARG ALA SEQRES 11 A 223 HIS GLN ALA ASN SER HIS LYS GLU ARG GLY TRP GLU GLN SEQRES 12 A 223 PHE THR ASP ALA VAL VAL SER TRP LEU ASN GLN ASN SER SEQRES 13 A 223 ASN GLY LEU VAL PHE LEU LEU TRP GLY SER TYR ALA GLN SEQRES 14 A 223 LYS LYS GLY SER ALA ILE ASP ARG LYS ARG HIS HIS VAL SEQRES 15 A 223 LEU GLN THR ALA HIS PRO SER PRO LEU SER VAL TYR ARG SEQRES 16 A 223 GLY PHE PHE GLY CYS ARG HIS PHE SER LYS THR ASN GLU SEQRES 17 A 223 LEU LEU GLN LYS SER GLY LYS LYS PRO ILE ASP TRP LYS SEQRES 18 A 223 GLU LEU
FORMUL 2 HOH *126(H2 O)
HELIX 1 1 GLY A 86 SER A 94 1 9 HELIX 2 2 SER A 94 LYS A 99 1 6 HELIX 3 3 LYS A 99 TYR A 116 1 18 HELIX 4 4 PRO A 121 VAL A 125 5 5 HELIX 5 5 PHE A 126 MET A 131 1 6 HELIX 6 6 ASP A 133 VAL A 137 5 5 HELIX 7 7 PRO A 167 ILE A 181 1 15 HELIX 8 8 LEU A 192 GLN A 198 1 7 HELIX 9 9 GLY A 221 SER A 237 1 17 HELIX 10 10 GLY A 246 GLY A 253 1 8 HELIX 11 11 SER A 273 GLY A 277 5 5 HELIX 12 12 ARG A 282 SER A 294 1 13
SHEET 1 A 2 VAL A 118 TYR A 119 0 SHEET 2 A 2 VAL A 209 ARG A 210 -1 O VAL A 209 N TYR A 119 SHEET 1 B 4 VAL A 200 ASN A 204 0 SHEET 2 B 4 VAL A 139 GLY A 143 1 N VAL A 139 O LEU A 201 SHEET 3 B 4 VAL A 241 TRP A 245 1 O LEU A 243 N VAL A 140 SHEET 4 B 4 HIS A 262 THR A 266 1 O HIS A 262 N PHE A 242
CISPEP 1 TYR A 119 PRO A 120 0 -0.33 CISPEP 2 ARG A 162 PRO A 163 0 0.06
CRYST1 47.511 54.771 78.071 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.021048 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018258 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012809 0.00000