HEADER LYASE 04-OCT-16 5H0K TITLE THE CRYSTAL STRUCTURE OF WT PEDOBACTER HEPARINUS SMUG2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEDOBACTER HEPARINUS DSM 2366; SOURCE 3 ORGANISM_TAXID: 485917; SOURCE 4 STRAIN: DSM 2366; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMUG, DNA DAMAGE, GLYCOSYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,W.CAO,P.PANG REVDAT 2 22-MAR-17 5H0K 1 JRNL REVDAT 1 18-JAN-17 5H0K 0 JRNL AUTH P.PANG,Y.YANG,J.LI,Z.WANG,W.CAO,W.XIE JRNL TITL SMUG2 DNA GLYCOSYLASE FROM PEDOBACTER HEPARINUS AS A NEW JRNL TITL 2 SUBFAMILY OF THE UDG SUPERFAMILY JRNL REF BIOCHEM. J. V. 474 923 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28049757 JRNL DOI 10.1042/BCJ20160934 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 11928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.6488 - 3.5612 1.00 2991 162 0.1840 0.2066 REMARK 3 2 3.5612 - 2.8269 1.00 2813 156 0.1991 0.2437 REMARK 3 3 2.8269 - 2.4696 1.00 2773 149 0.2168 0.2961 REMARK 3 4 2.4696 - 2.2438 0.99 2729 155 0.2365 0.3095 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1952 REMARK 3 ANGLE : 0.946 2634 REMARK 3 CHIRALITY : 0.058 276 REMARK 3 PLANARITY : 0.008 336 REMARK 3 DIHEDRAL : 12.436 1159 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5H0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.63900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 3350,0.25 M NACL, 0.1M TRIS REMARK 280 -HCL PH 8.5/0.1M HEPES PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.26950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.35700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.13475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.35700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 108.40425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.35700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.13475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.35700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.35700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 108.40425 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.26950 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 357 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 445 LIES ON A SPECIAL POSITION. 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 ALA A 235 REMARK 465 ILE A 236 REMARK 465 LEU A 237 REMARK 465 GLU A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 93 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 164 O HOH A 301 2.18 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 ILE A 62 -71.77 -104.62 REMARK 500 SER A 123 -158.90 -141.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H0J RELATED DB: PDB DBREF 5H0K A 1 236 UNP C6Y1J8 C6Y1J8_PEDHD 1 236 SEQADV 5H0K TYR A 65 UNP C6Y1J8 GLY 65 ENGINEERED MUTATION SEQADV 5H0K LEU A 237 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K GLU A 238 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 239 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 240 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 241 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 242 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 243 UNP C6Y1J8 EXPRESSION TAG SEQADV 5H0K HIS A 244 UNP C6Y1J8 EXPRESSION TAG SEQRES 1 A 244 MET MET THR PHE ALA ASP LYS VAL ILE GLN PHE ASN LYS SEQRES 2 A 244 ASP LEU SER TYR THR GLY SER THR LEU PRO PRO GLY ILE SEQRES 3 A 244 ARG ILE MET ASN PRO PHE LYS GLU HIS GLU GLN THR MET SEQRES 4 A 244 HIS ILE VAL GLU ALA PHE TYR HIS LYS TYR TYR ASN ASP SEQRES 5 A 244 ASN GLN SER ARG TYR LEU ILE LEU GLY ILE ASN PRO TYR SEQRES 6 A 244 ARG PHE GLY SER GLY LEU THR GLY ILE PRO PHE THR ASP SEQRES 7 A 244 PRO LYS ARG LEU ILE THR GLU CYS ASN ILE PRO TYR SER SEQRES 8 A 244 GLY LYS LEU SER HIS GLU PRO SER SER VAL PHE ILE TYR SEQRES 9 A 244 GLU MET ILE ASN ALA PHE GLY GLY ALA GLU ALA PHE TYR SEQRES 10 A 244 LYS GLN PHE TYR ILE SER SER PRO CYS PRO LEU GLY PHE SEQRES 11 A 244 THR SER ILE ALA ALA ASN GLY LYS GLU LYS ASN TYR ASN SEQRES 12 A 244 TYR TYR ASP SER LYS ALA LEU GLU LYS ALA VAL TYR GLU SEQRES 13 A 244 PHE ILE ILE GLU ASN ILE ARG LYS GLN LEU THR LEU GLY SEQRES 14 A 244 ILE THR THR ASP THR CYS PHE CYS LEU GLY THR GLY LYS SEQRES 15 A 244 ASN GLU LYS PHE LEU MET LYS VAL ASN ALA GLN TYR LYS SEQRES 16 A 244 PHE PHE LYS ARG ILE VAL ALA LEU GLU HIS PRO ARG PHE SEQRES 17 A 244 ILE MET GLN TYR LYS THR ALA SER LYS GLN PHE TYR ILE SEQRES 18 A 244 ASP LYS TYR ILE SER ALA PHE LYS ALA LEU ASN ASN SER SEQRES 19 A 244 ALA ILE LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *147(H2 O) HELIX 1 AA1 THR A 3 LEU A 15 1 13 HELIX 2 AA2 ASN A 30 HIS A 35 1 6 HELIX 3 AA3 GLU A 36 TYR A 50 1 15 HELIX 4 AA4 PHE A 67 THR A 72 5 6 HELIX 5 AA5 ASP A 78 GLU A 85 1 8 HELIX 6 AA6 GLU A 97 GLY A 111 1 15 HELIX 7 AA7 GLY A 112 GLN A 119 1 8 HELIX 8 AA8 SER A 147 THR A 167 1 21 HELIX 9 AA9 GLY A 181 LYS A 195 1 15 HELIX 10 AB1 HIS A 205 LYS A 213 1 9 HELIX 11 AB2 SER A 216 SER A 234 1 19 SHEET 1 AA1 3 ARG A 27 MET A 29 0 SHEET 2 AA1 3 GLY A 129 ILE A 133 -1 O GLY A 129 N MET A 29 SHEET 3 AA1 3 GLU A 139 ASN A 141 -1 O LYS A 140 N SER A 132 SHEET 1 AA2 4 PHE A 120 SER A 123 0 SHEET 2 AA2 4 ARG A 56 LEU A 60 1 N ILE A 59 O SER A 123 SHEET 3 AA2 4 ILE A 170 LEU A 178 1 O PHE A 176 N LEU A 60 SHEET 4 AA2 4 ARG A 199 LEU A 203 1 O LEU A 203 N CYS A 177 CRYST1 56.714 56.714 144.539 90.00 90.00 90.00 P 41 21 2 8 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 0.017632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006919 0.00000 MASTER 273 0 0 11 7 0 0 6 0 0 0 19 END