HEADER DNA BINDING PROTEIN 24-FEB-23 8IIM TITLE H109K MUTANT OF URACIL DNA GLYCOSYLASE X COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-4 URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.27; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 ATCC: 700084; SOURCE 6 GENE: MSMEG_0265; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS UDGX, H109K, MUTANT, PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.AROLI REVDAT 3 29-MAY-24 8IIM 1 REMARK REVDAT 2 02-AUG-23 8IIM 1 JRNL REVDAT 1 21-JUN-23 8IIM 0 JRNL AUTH S.AROLI,E.J.WOO,B.GOPAL,U.VARSHNEY JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSES OF UDGX: INSIGHTS INTO JRNL TITL 2 THE ACTIVE SITE POCKET ARCHITECTURE AND ITS EVOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 51 6554 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37283083 JRNL DOI 10.1093/NAR/GKAD486 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.2 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 25132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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 26.4100 - 3.3300 1.00 2812 143 0.1626 0.1656 REMARK 3 2 3.3300 - 2.6400 1.00 2768 143 0.1764 0.2105 REMARK 3 3 2.6400 - 2.3100 1.00 2770 139 0.1683 0.1933 REMARK 3 4 2.3100 - 2.1000 1.00 2730 147 0.1599 0.1638 REMARK 3 5 2.1000 - 1.9500 1.00 2744 149 0.1528 0.1692 REMARK 3 6 1.9500 - 1.8300 1.00 2735 135 0.1526 0.1775 REMARK 3 7 1.8300 - 1.7400 0.99 2725 137 0.1628 0.1961 REMARK 3 8 1.7400 - 1.6600 0.96 2635 124 0.1706 0.2073 REMARK 3 9 1.6600 - 1.6000 0.73 1997 99 0.1493 0.1806 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) : 16.760 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 : 0.008 1590 REMARK 3 ANGLE : 1.012 2160 REMARK 3 CHIRALITY : 0.064 247 REMARK 3 PLANARITY : 0.009 286 REMARK 3 DIHEDRAL : 5.777 228 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 8IIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.2 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 AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 52.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.11900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 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 (%): 45.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 0.1M BIS-TRIS PROPANE PH7.0, MICROBATCH, TEMPERATURE 295K 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 25.87500 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: 9790 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 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 GLU A 16 CG CD OE1 OE2 REMARK 470 GLU A 23 OE2 REMARK 470 ASP A 74 OD2 REMARK 470 ASP A 81 OD2 REMARK 470 ASP A 83 CG OD1 OD2 REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ASP A 165 OD2 REMARK 470 ASP A 166 CG OD1 OD2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 GLU A 189 OE2 REMARK 470 ASP A 206 CG OD1 OD2 REMARK 470 ARG A 208 CG CD NE CZ NH1 NH2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 585 DISTANCE = 7.07 ANGSTROMS REMARK 525 HOH A 586 DISTANCE = 9.31 ANGSTROMS 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 121.6 REMARK 620 3 SF4 A 301 S2 104.9 106.6 REMARK 620 4 SF4 A 301 S4 114.5 102.0 106.2 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 27 SG REMARK 620 2 SF4 A 301 S1 118.2 REMARK 620 3 SF4 A 301 S3 102.6 106.1 REMARK 620 4 SF4 A 301 S4 120.5 102.4 105.7 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 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S1 111.6 REMARK 620 3 SF4 A 301 S2 105.7 106.3 REMARK 620 4 SF4 A 301 S3 120.7 107.9 103.5 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 CYS A 120 SG REMARK 620 2 SF4 A 301 S2 113.7 REMARK 620 3 SF4 A 301 S3 114.8 103.8 REMARK 620 4 SF4 A 301 S4 111.9 106.4 105.5 REMARK 620 N 1 2 3 DBREF 8IIM A 1 208 UNP A0QP43 A0QP43_MYCS2 1 208 SEQADV 8IIM LYS A 109 UNP A0QP43 HIS 109 ENGINEERED MUTATION SEQRES 1 A 208 MET ALA GLY ALA GLN ASP PHE VAL PRO HIS THR ALA ASP SEQRES 2 A 208 LEU ALA GLU LEU ALA ALA ALA ALA GLY GLU CYS ARG GLY SEQRES 3 A 208 CYS GLY LEU TYR ARG ASP ALA THR GLN ALA VAL PHE GLY SEQRES 4 A 208 ALA GLY GLY ARG SER ALA ARG ILE MET MET ILE GLY GLU SEQRES 5 A 208 GLN PRO GLY ASP LYS GLU ASP LEU ALA GLY LEU PRO PHE SEQRES 6 A 208 VAL GLY PRO ALA GLY ARG LEU LEU ASP ARG ALA LEU GLU SEQRES 7 A 208 ALA ALA ASP ILE ASP ARG ASP ALA LEU TYR VAL THR ASN SEQRES 8 A 208 ALA VAL LYS HIS PHE LYS PHE THR ARG ALA ALA GLY GLY SEQRES 9 A 208 LYS ARG ARG ILE LYS LYS THR PRO SER ARG THR GLU VAL SEQRES 10 A 208 VAL ALA CYS ARG PRO TRP LEU ILE ALA GLU MET THR SER SEQRES 11 A 208 VAL GLU PRO ASP VAL VAL VAL LEU LEU GLY ALA THR ALA SEQRES 12 A 208 ALA LYS ALA LEU LEU GLY ASN ASP PHE ARG VAL THR GLN SEQRES 13 A 208 HIS ARG GLY GLU VAL LEU HIS VAL ASP ASP VAL PRO GLY SEQRES 14 A 208 ASP PRO ALA LEU VAL ALA THR VAL HIS PRO SER SER LEU SEQRES 15 A 208 LEU ARG GLY PRO LYS GLU GLU ARG GLU SER ALA PHE ALA SEQRES 16 A 208 GLY LEU VAL ASP ASP LEU ARG VAL ALA ALA ASP VAL ARG HET SF4 A 301 8 HET BME A 302 4 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 SF4 FE4 S4 FORMUL 3 BME C2 H6 O S FORMUL 4 HOH *186(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 TYR A 88 SHEET 3 AA1 4 VAL A 135 LEU A 139 1 O VAL A 137 N MET A 48 SHEET 4 AA1 4 ALA A 172 THR A 176 1 O THR A 176 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 LYS A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE3 SF4 A 301 1555 1555 2.31 LINK SG CYS A 27 FE2 SF4 A 301 1555 1555 2.30 LINK ND1 HIS A 95 FE4 SF4 A 301 1555 1555 2.23 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.25 CRYST1 36.450 51.750 54.630 90.00 104.83 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 0.027435 0.000000 0.007264 0.00000 SCALE2 0.000000 0.019324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018936 0.00000