PDB Short entry for 1EUG HEADER HYDROLASE 12-OCT-98 1EUG TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS TITLE 2 COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE TITLE 3 MECHANISM REVISITED COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (GLYCOSYLASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDG, UNG; COMPND 5 EC: 3.2.2.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 37762; SOURCE 4 STRAIN: B; SOURCE 5 GENE: UNG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 OTHER_DETAILS: SIGMA CHEMICAL KEYWDS GLYCOSYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.XIAO,M.TORDOVA,J.JAGADEESH,A.C.DROHAT,J.T.STIVERS,G.L.GILLILAND REVDAT 6 09-AUG-23 1EUG 1 SEQADV REVDAT 5 14-MAR-18 1EUG 1 SEQADV REVDAT 4 04-OCT-17 1EUG 1 REMARK REVDAT 3 13-JUL-11 1EUG 1 VERSN REVDAT 2 24-FEB-09 1EUG 1 VERSN REVDAT 1 12-OCT-99 1EUG 0 JRNL AUTH G.XIAO,M.TORDOVA,J.JAGADEESH,A.C.DROHAT,J.T.STIVERS, JRNL AUTH 2 G.L.GILLILAND JRNL TITL CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE JRNL TITL 2 AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND JRNL TITL 3 GLYCOSYLASE MECHANISM REVISITED. JRNL REF PROTEINS V. 35 13 1999 JRNL REFN ISSN 0887-3585 JRNL PMID 10090282 JRNL DOI 10.1002/(SICI)1097-0134(19990401)35:1<13::AID-PROT2>3.3.CO;2 JRNL DOI 2 -U REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 20TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.194 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1305 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24809 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.182 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1162 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21937 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 300 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2117.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8488 REMARK 3 NUMBER OF RESTRAINTS : 7462 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.041 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.050 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.012 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.060 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007026. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27664 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1UDG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION 14.9 MG/ML, 0.2 REMARK 280 M SODIUM ACETATE, 30% PEG4000, 0.1 M TRIS BUFFER, PH 8.5 USING REMARK 280 HANGING DROP AT 293K. 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 27.56500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.56500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.66000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 GLU A 4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 80 CD - NE - CZ ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 CYS A 200 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ASN A 201 C - N - CA ANGL. DEV. = -24.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 63 -81.12 -114.10 REMARK 500 GLN A 71 -72.33 -83.61 REMARK 500 HIS A 73 33.51 -148.08 REMARK 500 PHE A 77 -12.60 68.44 REMARK 500 THR A 99 -34.38 -133.30 REMARK 500 LEU A 139 -155.79 -80.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 1EUG A 1 229 UNP P12295 UNG_ECOLI 1 229 SEQADV 1EUG HIS A 213 UNP P12295 ARG 213 ENGINEERED MUTATION SEQRES 1 A 229 MET ALA ASN GLU LEU THR TRP HIS ASP VAL LEU ALA GLU SEQRES 2 A 229 GLU LYS GLN GLN PRO TYR PHE LEU ASN THR LEU GLN THR SEQRES 3 A 229 VAL ALA SER GLU ARG GLN SER GLY VAL THR ILE TYR PRO SEQRES 4 A 229 PRO GLN LYS ASP VAL PHE ASN ALA PHE ARG PHE THR GLU SEQRES 5 A 229 LEU GLY ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP PRO SEQRES 6 A 229 TYR HIS GLY PRO GLY GLN ALA HIS GLY LEU ALA PHE SER SEQRES 7 A 229 VAL ARG PRO GLY ILE ALA ILE PRO PRO SER LEU LEU ASN SEQRES 8 A 229 MET TYR LYS GLU LEU GLU ASN THR ILE PRO GLY PHE THR SEQRES 9 A 229 ARG PRO ASN HIS GLY TYR LEU GLU SER TRP ALA ARG GLN SEQRES 10 A 229 GLY VAL LEU LEU LEU ASN THR VAL LEU THR VAL ARG ALA SEQRES 11 A 229 GLY GLN ALA HIS SER HIS ALA SER LEU GLY TRP GLU THR SEQRES 12 A 229 PHE THR ASP LYS VAL ILE SER LEU ILE ASN GLN HIS ARG SEQRES 13 A 229 GLU GLY VAL VAL PHE LEU LEU TRP GLY SER HIS ALA GLN SEQRES 14 A 229 LYS LYS GLY ALA ILE ILE ASP LYS GLN ARG HIS HIS VAL SEQRES 15 A 229 LEU LYS ALA PRO HIS PRO SER PRO LEU SER ALA HIS ARG SEQRES 16 A 229 GLY PHE PHE GLY CYS ASN HIS PHE VAL LEU ALA ASN GLN SEQRES 17 A 229 TRP LEU GLU GLN HIS GLY GLU THR PRO ILE ASP TRP MET SEQRES 18 A 229 PRO VAL LEU PRO ALA GLU SER GLU FORMUL 2 HOH *300(H2 O) HELIX 1 1 TRP A 7 LEU A 11 1 5 HELIX 2 2 GLU A 14 GLN A 16 5 3 HELIX 3 3 PRO A 18 GLN A 32 1 15 HELIX 4 4 GLN A 41 ASP A 43 5 3 HELIX 5 5 ASN A 46 PHE A 50 1 5 HELIX 6 6 LEU A 53 ASP A 55 5 3 HELIX 7 7 PRO A 87 GLU A 97 1 11 HELIX 8 8 GLU A 112 GLN A 117 1 6 HELIX 9 9 TRP A 141 HIS A 155 1 15 HELIX 10 10 SER A 166 LYS A 171 1 6 HELIX 11 11 ALA A 193 ARG A 195 5 3 HELIX 12 12 HIS A 202 GLN A 212 1 11 SHEET 1 A 4 VAL A 119 ASN A 123 0 SHEET 2 A 4 VAL A 58 GLY A 62 1 N VAL A 58 O LEU A 120 SHEET 3 A 4 VAL A 160 TRP A 164 1 N VAL A 160 O VAL A 59 SHEET 4 A 4 HIS A 181 ALA A 185 1 N HIS A 181 O PHE A 161 CISPEP 1 TYR A 38 PRO A 39 0 -6.42 CRYST1 55.130 61.320 64.400 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 0.018139 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015528 0.00000