HEADER DNA BINDING PROTEIN 24-AUG-18 6AIL TITLE CRYSTAL STRUCTURE AT 1.3 ANGSTROMS RESOLUTION OF A NOVEL UDG, UDGX, TITLE 2 FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL DNA GLYCOSYLASE X; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ASP165, ASP166, AND PRO209 COULD NOT BE MODELED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS STR. MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA REPAIR, BASE EXCISION, DNA-PROTEIN CROSSLINK., DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.C.AHN,S.AROLI,V.VARSHNEY,E.J.WOO REVDAT 2 27-MAR-24 6AIL 1 REMARK REVDAT 1 29-MAY-19 6AIL 0 JRNL AUTH W.C.AHN,S.AROLI,J.H.KIM,J.H.MOON,G.S.LEE,M.H.LEE,P.B.SANG, JRNL AUTH 2 B.H.OH,U.VARSHNEY,E.J.WOO JRNL TITL COVALENT BINDING OF URACIL DNA GLYCOSYLASE UDGX TO ABASIC JRNL TITL 2 DNA UPON URACIL EXCISION. JRNL REF NAT.CHEM.BIOL. V. 15 607 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31101917 JRNL DOI 10.1038/S41589-019-0289-3 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 42199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 28.1122 - 3.2164 0.92 2826 148 0.1688 0.1884 REMARK 3 2 3.2164 - 2.5535 0.99 2998 145 0.1541 0.1633 REMARK 3 3 2.5535 - 2.2308 0.99 2969 145 0.1349 0.1370 REMARK 3 4 2.2308 - 2.0269 0.98 2935 148 0.1250 0.1511 REMARK 3 5 2.0269 - 1.8817 0.98 2969 145 0.1162 0.1557 REMARK 3 6 1.8817 - 1.7708 0.98 2932 149 0.1135 0.1329 REMARK 3 7 1.7708 - 1.6821 0.97 2907 147 0.1135 0.1280 REMARK 3 8 1.6821 - 1.6089 0.97 2901 145 0.1041 0.1365 REMARK 3 9 1.6089 - 1.5469 0.97 2899 141 0.1009 0.1457 REMARK 3 10 1.5469 - 1.4936 0.96 2869 145 0.1086 0.1516 REMARK 3 11 1.4936 - 1.4469 0.96 2862 138 0.1121 0.1373 REMARK 3 12 1.4469 - 1.4055 0.96 2837 143 0.1140 0.1635 REMARK 3 13 1.4055 - 1.3685 0.95 2866 139 0.1176 0.1549 REMARK 3 14 1.3685 - 1.3351 0.81 2427 124 0.1262 0.1686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.370 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 : 0.009 1576 REMARK 3 ANGLE : 0.932 2137 REMARK 3 CHIRALITY : 0.074 241 REMARK 3 PLANARITY : 0.007 282 REMARK 3 DIHEDRAL : 20.638 576 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 6AIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 190 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42217 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.335 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 (%) : 96.2 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 55.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 0.1M BIS-TRIS PROPANE PH7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.81900 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ASP A 165 REMARK 465 ASP A 166 REMARK 465 PRO A 209 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 HH21 ARG A 46 O VAL A 207 1.51 REMARK 500 O HOH A 435 O HOH A 459 1.78 REMARK 500 O HOH A 530 O HOH A 555 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 SF4 A 301 S1 115.2 REMARK 620 3 SF4 A 301 S2 120.1 103.0 REMARK 620 4 SF4 A 301 S4 104.2 106.4 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 27 SG REMARK 620 2 SF4 A 301 S1 121.8 REMARK 620 3 SF4 A 301 S2 119.1 102.3 REMARK 620 4 SF4 A 301 S3 101.0 105.3 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S2 105.2 REMARK 620 3 SF4 A 301 S3 123.1 107.1 REMARK 620 4 SF4 A 301 S4 109.7 105.8 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 SF4 A 301 S1 111.6 REMARK 620 3 SF4 A 301 S3 115.9 105.2 REMARK 620 4 SF4 A 301 S4 113.2 105.6 104.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 301 DBREF 6AIL A 1 209 UNP A0QP43 A0QP43_MYCS2 1 209 SEQRES 1 A 229 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 229 LEU VAL PRO ARG GLY SER HIS MET ALA GLY ALA GLN ASP SEQRES 3 A 229 PHE VAL PRO HIS THR ALA ASP LEU ALA GLU LEU ALA ALA SEQRES 4 A 229 ALA ALA GLY GLU CYS ARG GLY CYS GLY LEU TYR ARG ASP SEQRES 5 A 229 ALA THR GLN ALA VAL PHE GLY ALA GLY GLY ARG SER ALA SEQRES 6 A 229 ARG ILE MET MET ILE GLY GLU GLN PRO GLY ASP LYS GLU SEQRES 7 A 229 ASP LEU ALA GLY LEU PRO PHE VAL GLY PRO ALA GLY ARG SEQRES 8 A 229 LEU LEU ASP ARG ALA LEU GLU ALA ALA ASP ILE ASP ARG SEQRES 9 A 229 ASP ALA LEU TYR VAL THR ASN ALA VAL LYS HIS PHE LYS SEQRES 10 A 229 PHE THR ARG ALA ALA GLY GLY LYS ARG ARG ILE HIS LYS SEQRES 11 A 229 THR PRO SER ARG THR GLU VAL VAL ALA CYS ARG PRO TRP SEQRES 12 A 229 LEU ILE ALA GLU MET THR SER VAL GLU PRO ASP VAL VAL SEQRES 13 A 229 VAL LEU LEU GLY ALA THR ALA ALA LYS ALA LEU LEU GLY SEQRES 14 A 229 ASN ASP PHE ARG VAL THR GLN HIS ARG GLY GLU VAL LEU SEQRES 15 A 229 HIS VAL ASP ASP VAL PRO GLY ASP PRO ALA LEU VAL ALA SEQRES 16 A 229 THR VAL HIS PRO SER SER LEU LEU ARG GLY PRO LYS GLU SEQRES 17 A 229 GLU ARG GLU SER ALA PHE ALA GLY LEU VAL ASP ASP LEU SEQRES 18 A 229 ARG VAL ALA ALA ASP VAL ARG PRO HET SF4 A 301 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *190(H2 O) HELIX 1 AA1 ALA A 4 VAL A 8 5 5 HELIX 2 AA2 ASP A 13 GLY A 22 1 10 HELIX 3 AA3 CYS A 27 ARG A 31 5 5 HELIX 4 AA4 GLY A 55 GLY A 62 1 8 HELIX 5 AA5 GLY A 67 ALA A 80 1 14 HELIX 6 AA6 ASP A 83 LEU A 87 5 5 HELIX 7 AA7 SER A 113 GLU A 132 1 20 HELIX 8 AA8 GLY A 140 GLY A 149 1 10 HELIX 9 AA9 ARG A 153 HIS A 157 5 5 HELIX 10 AB1 HIS A 178 LEU A 183 5 6 HELIX 11 AB2 PRO A 186 ASP A 206 1 21 SHEET 1 AA1 4 TYR A 88 ASN A 91 0 SHEET 2 AA1 4 ILE A 47 GLY A 51 1 N MET A 49 O THR A 90 SHEET 3 AA1 4 VAL A 135 LEU A 139 1 O LEU A 139 N ILE A 50 SHEET 4 AA1 4 ALA A 172 THR A 176 1 O VAL A 174 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 HIS A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE3 SF4 A 301 1555 1555 2.33 LINK SG CYS A 27 FE4 SF4 A 301 1555 1555 2.31 LINK ND1 HIS A 95 FE1 SF4 A 301 1555 1555 2.06 LINK SG CYS A 120 FE2 SF4 A 301 1555 1555 2.25 SITE 1 AC1 6 CYS A 24 GLY A 26 CYS A 27 VAL A 93 SITE 2 AC1 6 HIS A 95 CYS A 120 CRYST1 36.326 51.638 54.362 90.00 105.31 90.00 P 1 21 1 2 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 0.027528 0.000000 0.007537 0.00000 SCALE2 0.000000 0.019366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019072 0.00000